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Flashcards in MICR 200A Deck (317):

What does a circular colony look like?

> 1 mm in diameter, with an unbroken/even round edge.


In bacterial cell division, which happens first: formation of the divisome, or elongation and DNA replication?

Elongation and DNA replication.


Define proteomics.

A subdiscipline of genomics studying patterns of protein expression in cells.


What category of oral bacteria adhere to enamel?

Facultative aerobes.


What eukaryotic protein is FtsA closely related to?



What does an irregular colony look like?

Uneven or indented around the edge.


Define enzyme.

A catalyst, usually made of protein, that promotes specific reactions or groups of reactions.


Define defined medium.

Any culture medium whose exact chemical composition is known.


Define RNA.

Ribonucleic acid: a polymer of nucleotides connected via a phosphate-ribose backbone, involved in protein synthesis or as genetic material of some viruses.


What is the focus of microbial physiology?

Nutrition and metabolism.


What does a pink Gram stain indicate?

Gram-negative: lipopolysaccharide (LPS) is the main component of the cell wall.


Define supportive media.

A (complex) culture media with ingredients that allow growth of a wide variety of microbes.


Define chemolithotroph.

An organism that obtains its energy from the oxidation of inorganic compounds.


How is the cell division plane formed in bacterial cells?

FtsZ proteins attach in a ring precisely around the centre of the cell, determining the site of division.


What is the focus of medicinal microbiology?

Infectious disease.


Define codon.

A sequence of 3 nitrogenous bases in mRNA that encodes a specific amino acid.


What 3 factors affect the dynamic state of the normal human microflora?

Diet, environment, and contact with other people.


What does a spindle colony look like?

Growth that develops within the media (anaerobic).


Define culture (microbiology).

A particular strain or kind of organism growing in a laboratory medium.


Define thermal death time.

The time it takes to kill all cells in a population at a given temperature.


What is the role of pigments in phototrophic organisms?

Pigments allow the capture of light and the conversion of light energy to chemical energy.


What is the purpose of bile salts added to selective culture media?

Bile salts inhibit growth of Gram-positive microbes.


Define differential medium.

A culture medium with an indicator (usually a dye) added which reveals whether a particular metabolic reaction has occurred during growth.


Define pure culture (microbiology).

A culture containing a single kind of microorganism.


Define pathogen.

A disease-causing microorganism.


What is the focus of immunology?

Immune systems.


Where do most microbial cells live on Earth?

In oceanic and terrestrial subsurfaces, up to 10 km deep (more oceanic than terrestrial).


What is the medical significance of understanding bacterial cell division?

Understanding the roles of bacteria-specific proteins involved in division can lead to drug design targeting specific stages of growth in pathogenic bacteria.


How does immersion oil allow for greater magnification in light microscopy?

The oil increases the light-gathering ability of the lens by letting some light rays coming through the specimen at angles to be collected and viewed.



Define generation.

The separation event of 1 cell dividing into 2 daughter cells.


Define group translocation.

A method of nutrient uptake in which molecules are modified as they are transported across a membrane, so it's a different molecule on either side.


Define free energy.

Energy available to do work.


How are Koch's postulates used to link a suspected pathogen to a disease?

The pathogen must be present in all cases of disease and absent in healthy animals; when grown in pure culture and given to healthy animals, must cause disease; when subsequently reisolated, must be shown to be the same as the original pathogen.


What are the thinnest fibres in the eukaryotic cytoskeleton?



Which 3 Min proteins are involved in bacterial cell division?

MinC, MinD, and MinE.


When did microbial cells first appear?

~3.8-3.9 billion years ago.


How do MinC, MinD, and MinE work to localize FtsZ ring formation during bacterial cell division?

  • MinC/D form a helix encircling the inner cytoplasmic membrane that oscillates from pole to pole of the cell, inhibiting FtsZ binding wherever they go
  • MinE also oscillates from pole to pole, sweeping C/D aside
  • Combined oscillation = MinC/D concentrated at poles: cell centre becomes most permissive FtsZ binding site


How do you focus the field diaphragm (turning the circle of light into a heptagon) for Koehler illumination?

By adjusting the height of the condenser.


Which 2 classes of macromolecules contain most of a cell's nitrogen?

Proteins and nucleic acids.


What is the purpose of antibiotics added to selective culture media?

Antibiotics favour growth of antibiotic-resistant microbes.


Why are autotrophs also called primary producers?

They synthesize new organic material from CO2 (inorganic carbon).


What colony shape is this?



What is the difference between rhizoid and filamentous microbial colonies?

Both are characterized by thin projections from the colony centre, but filamentous projections are individual while rhizoid (root-like) projections are branched.


Which nitrogenous bases are purines?

Adenine and guanine.


Which requires inhibitory or lysing agents: decontamination or disinfection?



Define genetic exchange.

Transfer or acceptance of genes between neighbouring cells, either of the same or of different species; many prokaryotes can do this.


Which relies on population size: thermal death time, decimal reduction time, both, neither?

Thermal death time: it takes longer to kill all cells in a large population than in a small one. Decimal reduction time is independent of initial population size, as it is a proportional measure.


Define generation time.

The time required for a cell population to double, or for 1 parent cell to separate into 2 daughter cells.


What does a purple Gram stain indicate?

Gram-positive: peptidoglycan is the main component of the cell wall.


What is the focus of molecular biology?

Nucleic acids and proteins.


Define microtubule.

A filamentous (tubular) eukaryotic polymer made of α- and β-tubulin with functions relating to cell shape and motility.


What are the 2 major forms of phototrophy known in prokaryotes?

Oxygenic (O2-producing) and anoxygenic (non-O2-producing) photosynthesis.


Which is the most common method of microbial control?



Define differential stain (microscopy).

A stain that renders different kinds of cells different colours (e.g. Gram stain).


Which is more relevant to bioenergetic calculations: ΔG or ΔG0'? Why?

ΔG: this represents the free energy change between reactants and products under the actual reaction conditions.


Define enrichment culture technique.

The use of selective culture media and incubation conditions to isolate specific microorganisms from natural samples by favouring specific metabolic groups.


Define heterotroph.

An organism that obtains cell carbon from some organic material.


What does it mean if ΔG0' is positive?

The reaction is endergonic, requiring energy in order to proceed.


Define microbial community.

2 or more populations of cells that coexist and interact in a habitat.


What are the resolution and magnification limits of light microscopes?

Resolution: ~0.2 μm; magnification: ~2000x.


What is the focus of biotechnology?

Production of human proteins by genetically engineered microorganisms.


What are the 3 stages of genetic information flow in a cell?

Replication, transcription, and translation.


What happens during DNA replication?

DNA polymerase duplicates the double helix to make 2 copies.


What is the focus of industrial microbiology?

Large-scale production of antibiotics, alcohols, and other chemicals.


Define decontamination.

Treatment of an object or inanimate surface to make it safe to handle.


Which domains of life are prokaryotic?

Bacteria and Archaea.


Define rumen.

A microbial ecosystem in the gut of ruminant animals where large populations of microorganisms digest and ferment cellulose, allowing ruminants to thrive on otherwise nutrient-poor plant food.


During bacterial cell division, what happens to the FtsZ ring when the cell begins to constrict?

The FtsZ ring begins to depolymerize (fuelled by hydrolyzation of GTP), triggering septum formation to seal off the daughter cells from one another.


Define septum (binary fission).

A partition resulting from inward growth of the cell wall and cytoplasmic membrane from opposing directions.


What category of oral bacteria adher below the gumline?

Obligate anaerobes.


What basic cellular processes are common to all cell types?

Metabolism (genetic & catalytic processes), growth (by cell division), and evolution.


What are the 3 major functions of microtubules in eukaryotes?

  • Maintain cell shape/motility by cilia/flagella
  • Move chromosomes during mitosis
  • Move organelles within the cell


Define free energy of formation.

The energy released or required during the formation of a given molecule from its component elements.


What is the difference between prokaryotic and eukaryotic genomes?

Prokaryotes have DNA as a closed circular chromosome (or sometimes linear) aggregated into a nucleoid region; eukaryotes have linear DNA within a membrane-enclosed nucleus.


What happens during transcription?

Genetic information is transferred from DNA to RNA by RNA polymerase.


How are Bacteria and Archaea related phylogenetically?

They're not - they are phylogenetically distinct despite sharing many structural features. Archaea are more closely related to Eukarya than to Bacteria.


What 3 classes of proteins are involved in translating codons into sequences of amino acids?

Ribosomes, transfer RNA (tRNA), and translation factors (helper proteins).


What is the focus of microbial genetics?

Genes, heredity, and genetic variation.


Why can chemoliphotrophs and chemooorganotrophs live in close association with one another?

They don't compete with each other for electron/energy sources, and the inorganic waste products of chemoorganotrophs can often serve as electron/energy sources for chemolithotrophs.


What conditions offer the best resolution in light microscopy?

Blue light (short wavelength) and a lens with a very high numerical aperture (light-gathering ability).


Define chemoorganotroph.

An organism that obtains its energy from the oxidation of organic compounds.


Define growth (cellular).

An increase in cell count as a result of cell division.


What is the significance of understanding the mode of replication in L-form B. subtilis?

It is likely how ancient cells reproduced.


Define metabolism.

All biochemical reactions in a cell.


What does a smooth colony edge look like?

Sharply defined and even/entire, with no notches or projections.


What is the focus of genomics?

Genome sequencing and comparative analysis.


How do plasmids replicate during cell division?

They are independent of chromosomal DNA and their replication is thus not tied to cellular replication, but they often replicate during cell division in response to the lower concentration of plasmids in the resulting cytoplasm.


Define nucleoid.

The aggregated mass of DNA that makes up the chromosome of prokaryotic cells.


How does blood agar work as a differential culture media?

The surrounding media will be greenish around α-hemolytic colonies and clear around β-hemolytic colonies.


Which nitrogenous bases form the most thermodynamically favourable H-bonds with each other?

Adenine-thymine (AT) and guanine-cytosine (GC).


What is the difference between eukaryotic and prokaryotic transcription?

In eukaryotes, each gene is transcribed to yield a single mRNA; in prokaryotes, a single mRNA molecule may contain information from several genes.


Define sterilization.

The killing or removal of all microorganisms (including viruses).


Why are organic compounds used to make dyes for microscopy stains?

Using organic compounds allows each class of dye to have an affinity for specific cellular materials.


Define septation.

The formation of a new wall between daughter cells.


Define chemolithotroph.

An autotrophic organism that obtains its energy from oxidation of inorganic compounds (usually obtaining C from CO2).


Define divisome.

A complex of Fts proteins that directs bacterial cell division.


When graphing heat sterilization, what kind of function is heat-killing? What does that mean?

First-order (exponential): heat-killing proceeds more rapidly as the temperature rises.


Define simple medium.

Any culture medium that only contains a single carbon source.


What is the focus of microbial ecology?

Microbial diversity, activity, and biogeochemistry.


In light microscopes, how are numerical aperture and magnification related?

Lenses with greater magnification tend to have a higher numerical aperture, i.e. can gather more light.


In setting up for Koehler illumination, what should you focus first: the ink mark or the field diaphragm?

The ink mark: adjust the stage (coarse, then fine focus) to focus on the mark before adjusting for the light.


What are 2 common examples of asymmetrical cell division?

Budding and endospore formation.


What are standard conditions (as indicated by 0')?

pH 7, 25 ºC, 1 atm, with all reactants and products at molar concentrations.


Which 2 classes of macromolecules make up most of a cell's dry weight?

Proteins and RNA.


What does a rhizoid colony look like?

A root-like, spreading growth.


How is the replication process of the L-form of B. subtilis unique among microorganisms?

It has no peptidoglycan layer, so it needs to be osmotically protected from lysis at all stages; it reproduces by budding off in protective bubbles (not by binary fission).


How is a poured agar culture prepared?

Mix liquid culture with cooled liquid agar, then pour into a plate or tube for cells to be grown in suspension.


Define complex medium.

Any culture medium whose precise chemical composition is unknown.


Which groups of microorganisms are characterized by anoxygenic photosynthesis?

Green bacteria, purple bacteria, and heliobacteria.


What does the Fts in Fts protein stand for?

Filamenting temperature-sensitive.


Which type of culture media is easiest to prepare? Why?

Complex: the precise chemical composition is unknown, and the media can be prepared from commercially available dehydrated mixes that provide nutrients allowing growth of a wide variety of organisms with no extra prep required.


How does slant agar work as a differential media?

Liquid culture is streaked across the solid agar surface, then punched down into the tube: growth on the surface is aerobic, and growth within the tube is anaerobic.


Define ribosome.

A structure composed of RNAs and proteins upon which new proteins are made.


What are the 3 domains of life?

Bacteria, Archaea, and Eukarya.


Define resolution (microscopy).

The ability to distinguish 2 adjacent objects as distinct and separate.


What is the focus of agricultural/soil microbiology?

Microbial diversity and processes in soil.


What vaccine did Louis Pasteur develop?

Rabies (1885).


Define metabolomics.

A subdiscipline of genomics studying patterns of metabolic pathway expression in cells.


Define transcriptomics.

A subdiscipline of genomics studying patterns of RNA expression in cells.


Define phototroph.

An organism that obtains its energy from light (rather than relying on chemicals).


What is the difference between plasmid and chromosomal DNA in prokaryotes?

Plasmid genes usually give the cell some special property not essential to all growth conditions; chromosomal genes are needed for basic survival.


What is the function of the completed divisome in a bacterial cell?

It orchestrates the synthesis of cytoplasmic membrane and cell wall material at the centre of the elongating cell until the cell has doubled in size and is ready to separate.


What colony shape is this?



Define tRNA.

Transfer RNA: a small RNA molecule used in translation that has an anticodon at one end and its corresponding amino acid at the other end.


Define autotroph.

An organism that obtains cell carbon from CO2.


Define cytoplasm.

The fluid portion of a cell, bounded by the cell membrane, containing an aqueous mixture of macromolecules, small organic molecules, inorganic ions, and ribosomes.


Define enriched medium.

A culture medium that starts out as a complex medium and is embellished with additional highly nutritious substances (e.g. serum, blood) for nutritionally demanding organisms.


Define cytoplasmic membrane.

A semipermeable barrier that separates the cell interior (cytoplasm) from the environment.


What are the 2 major structural differences between microtubules and microfilaments?

  • Microtubules are larger than microfilaments (~24 nm vs ~6 nm in diameter)
  • Microtubules are made of tubulin; microfilaments are made of actin


Which 4 elements make up most of a cell's dry weight?

C, O, N, and H.


How do microbes in the human GI tract help us?

By synthesizing vitamins and other nutrients, and by outcompeting pathogenic microbes.


How does bright-field light microscopy work?

Specimens are visualized by slight differences in contrast between them and their surroundings (as cells absorb or scatter light to varying degrees).


What is the focus of virology?

Viruses and subviral particles.


What types of organisms typically have cell walls?

Plants and most microorganisms have cell walls; animal cells (with rare exceptions) do not.


What is the focus of aquatic microbiology?

Microbial processes in water and wastewater, and drinking water safety.


What eukaryotic proteins are bacterial Fts proteins related to?

Tubulin proteins (involved in making eukaryotic microtubules).


Define chemotroph.

An organism that obtains its energy from chemicals (as opposed to light).


Define organelle.

A bilayer membrane-enclosed structure found in eukaryotic cells.


Define prokaryote.

A cell or organism with no nucleus or other membrane-enclosed organelles, usually with DNA in a single circular chromosome.


Which microbial organisms are the ancestors of plant and animals?

Microbial Eukarya.


Define cell wall.

A rigid layer present outside the cytoplasmic membrane that gives the cell structural strength and protection from osmotic lysis.


What is the focus of microbial systematics?

Classification and nomenclature.


What is the collective function of Min proteins during bacterial cell division?

They interact to help guide FtsZ proteins to the cell centre for divisome formation.


What are the only real challenges faced by oral bacteria?

Lysozyme (from saliva) and mechanical disruption.


Why are positively-charged basic dyes good general purpose microscopy stains?

Cell surfaces are usually negatively charged, so basic dyes have a high affinity for them.


Define DNA.

Deoxyribonucleic acid: a polymer of nucleotides connected via a phosphate-deoxyribose sugar backbone; the genetic material of cells and some viruses.


Which type of culture media is best for performing an initial survey of microbes?

Complex supportive media.


Define chemolithotroph.

An organism that obtains its energy from the oxidation of inorganic compounds.


What colony shape is this?



Define disinfection.

The elimination of pathogens from inanimate objects or surfaces.


Define Fts proteins.

A series of proteins found in all bacteria with essential roles in cell division.


What does ΔGC represent?

The change in free energy between reactants and products in a reaction carried out under standard conditions (pH 7, 25 °C, 1 atm, molar concentrations of reactants and products).


What are the 3 major types of microbial ecosystems?

Aquatic (marine, freshwater, ice, hot springs, etc.), terrestrial (surface to deep subsurface), and higher organisms (in/on plants/animals).


What are 3 common basic dyes in microscopy?

Methylene blue, crystal violet, and safranin.


How can a simple defined media be used as a selective media?

A simple defined media by definition only includes a single carbon source, so it will allow growth of organisms that can use that carbon source while inhibiting the growth of those that can't.


Define gene.

A segment of DNA (or RNA) specifying a particular protein or polypeptide chain, or a tRNA or rRNA; a unit of heredity.


Define sterile (microbiology).

Free of all living organisms and viruses.


What colony shape is this?



Where are the major and minor grooves on the DNA double helix? Where do most specifically DNA-binding proteins interact?

Most proteins that bind DNA bind in the major groove, where there is more space.


Define eukaryote.

A cell or organism with a membrane-enclosed nucleus and (usually) other organelles.


Define methanotroph.

An organism that can recycle methane back to CO2.


What is the difference between genetic exchange and evolution?

Genetic exchange is independent of evolution and can significantly accelerate adaptation to new habitats or changing conditions regardless of selective pressures.


Which domains of life are eukaryotic?



Which groups of microorganisms are characterized by oxygenic photosynthesis?

Cyanobacteria (prokaryotes) and algae (eukaryotes).


Under ideal conditions, what is the generation time for E. coli?

20 minutes.


What happens during translation?

Proteins are synthesized using genetic information from mRNA.


What are the 2 phases of the bacterial cell cycle?

  1. Replication and partitioning of DNA
  2. Cytokinesis


For any light microscope lens, what is the diameter of the smallest object resolvable by that lens?

[0.5 x (wavelength of light used)] ÷ (numerical aperture)


How do cells get energy to make new structures?

All cells take up nutrients from the environment and transform them chemically into new materials and waste products; the energy conserved from those transformations is used to build structures.


What does it mean if ΔG0' is negative?

The reaction is exergonic and will release energy.


How does penicillin kill bacterial cells?

By targeting proteins involved in cell division (e.g. FtsI) and inhibiting their activity, thus preventing division.


What does a filamentous colony look like?

Long, irregular, interwoven threads (mold-like).


During bacterial cell division, where does the energy come from that is required for FtsZ ring polymerization and depolymerization?

Enzymatic activity of FtsZ hydrolyzes GTP, yielding the required energy.


Define LUCA.

Last universal common ancestor; a common ancestral cell from which all cells descended.


In bacterial cell division, why must DNA be replicated before the FtsZ can form?

The FtsZ ring forms in the space between the newly separated nucleoids; untl they have separated, the forming nucleoids block ring formation.


What colony shape is this?



Which nitrogenous bases are pyrimidines?

Thymine, cytosine, and uracil.


Define nucleotide.

A monomeric unit of nucleic acid, consisting of a sugar, a phosphate, and a nitrogenous base (purine or pyrimidine).


What does a punctiform colony look like?

Pinpoint colonies, < 1 mm in diameter.


What is the difference between prokaryotic and eukaryotic chromosomes?

Prokaryotes typically have a single chromosome consisting of a circular DNA molecule; eukaryotes typically have several chromosomes, each containing a linear DNA molecule.


Which genera are often found in the mouth?

Streptococcus, Haemophilus, Veillonella, Actinomyces, and Fusobacterium (plus a few archaea and yeast).


Define FtsZ protein.

A bacterial cell division protein that forms a ring along the mid-cell division plane to initiate cell division.


Define normal microflora/microbiome.

Dynamic communities of bacteria found in human surface tissues that are readily colonized during and after birth.


Define decimal reduction time.

The time required for a 10-fold reduction in the viability of a microbial population at a given temperature or concentration of antimicrobial agent.


Where do animal methane emissions come from?

Methane-producing archaea living in animal guts.


Define plasmid.

A small circle of DNA distinct from that of the prokaryotic chromosome/nucleoid.


What is the purpose of staining for bright-field light microscopy?

To increase the contrast between the specimen and its surroundings for better viewing.


What colony shape is this (found within the media)?



What is the focus of microbial biochemistry?

Enzymes and chemical reactions in cells.


How is ΔG0' calculated for the reaction A + B ⇄ C + D from corresponding ΔGf0 values?


Define microfilament.

A filamentous polymer of the protein actin with roles in cell shape, amoeboid motility, and cell division in eukaryotic cells.


Why do microbial cells probably grow much slower in nature than they do in lab conditions?

  • The conditions and resources provided for optimal growth in lab may not be present in nature
  • In nature, there is competition between different species in microbial communities for resources and space


What is the fastest observed generation time in microbes?

6 minutes.


What is the most common range of generation times for most microorganisms?

Hours or days.


Define Koch's postulates.

A set of rigorous criteria for definitively linking cause &amp; effect in an infections disease.


Define genetic element.

A structure that carries genetic information, such as a chromosome, a plasmid, or a virus genome.


What level of identification is possible from culturing microbes on blood agar?

Blood agar is used to differentiate between α-, β-, and γ-hemolysis and can be used to identify microbes to genus.


Why is the chemical makeup of a cell generally measured in terms of dry weight?

Cells are 70-80% water, which would skew the H and O count.


Define chromosome.

A genetic element carrying genes essential to cellular function.


Define rRNA.

Ribosomal RNA: the types of RNA found in the ribosome, some of which may participate actively in protein synthesis.


Define selective medium.

A culture medium that contains compounds that inhibit the growth of some microorganisms but not others.


What are the 5 steps of cytokinesis?

  1. Site selection
  2. Assembly of FtsZ ring
  3. Linkage of FtsZ ring to plasma membrane or other cell wall components
  4. Assembly of synthesis apparatus
  5. Constriction of cell and/or septum formation


What is the function of most trace elements?

Enzyme cofactors.


Define nodules.

Structures on legume roots filled with bacteria that convert atmospheric N to ammonia, giving the plants a source of N for growth.


What types of genes are especially good markers of microbial diversity?

Ribosomal RNA.


Define balanced growth.

A stage within a single generation when all cellular constitutents are increasing proportionally in preparation for cell division.


Define numerical aperture.

A measure of the light-gathering ability of an objective lens in a light microscope.


Define catabolism.

Biochemical processes involved in the breakdown of organic or inorganic compounds, usually leading to the production of energy.


What is the function of the protein ZipA?

During bacterial cell division, ZipA anchors FtsZ to the cytoplasmic membrane and stabilizes it as the divisome forms.


What is the function of DNA gyrase?

DNA gyrase is a topoisomerase in bacteria and archaea that inserts negative supercoils into DNA by making double-strand breaks.


Which 2 classes of antibiotics target DNA gyrase? Why is it a good drug target?

Quinolones and fluoroquinolones; DNA gyrase is involved in supercoiling bacterial/archaeal chromosomes, so inhibiting its activity means the cell can't maintain DNA structure.


Define transposable element.

A segment of DNA that can move from 1 site on a DNA molecule to another, either within the same molecule or between 2 different molecules.


Define operon.

1 or more genes transcribed into a single mRNA and under the control of a single regulatory site.


Are operons found in prokaryotic or eukaryotic cells?

Prokaryotic cells only: eukaryotic cells have a single mRNA for each gene.


How are plasmids both independent of and dependent on chromosomal DNA?

Plasmids have their own origin of replication, but they rely on chromosomally encoded enzymes for the actual replication process.


Define copy number.

The number of plasmids of a particular type within a cell, as determined by plasmid genes and by host-plasmid interactions.


Define resistance plasmid (R-plasmid).

A class of plasmids that confer resistance to antibiotics and other growth inhibitors, usually with genes encoding proteins that either inactivate the antibiotic or protect the cell by some other mechanism.


What 2 major virulence factors of pathogens are usually encoded in plasmids?

  • The pathogen's ability to attach to and colonize specific host tissues
  • Production of toxins, enzymes, and other molecules that damage the host


Define bacteriocin.

An agent produced by certain bacteria that inhibits or kills closely related species.


What is the main functional difference between antibiotics and bacteriocins?

Bacteriocins have a much narrower range of activity: a bacteriocin produced by a specific bacterium only targets closely related species of bacteria.


Define semiconservative replication.

DNA synthesis yielding new double helices, each consisting of 1 parental and 1 progeny strand.


In which direction does DNA replication always proceed? Why?

5' to 3': addition of an incoming nucleotide requires a free hydroxyl group, which is only available at the 3' end. (The 5'-phosphate of the incoming nucleotide is attached to the 3'-hydroxyl of the previously added nucleotide.)


Define DNA polymerase.

A class of enzymes that catalyze the addition of deoxynucleotides, involved in DNA replication and repair.


Define primer.

A short length of RNA (or DNA) used to initiate synthesis of a new DNA strand.


Define primase.

An enzyme that synthesizes a short RNA primer from the opening of the double helix at the beginning of DNA replication.


Why does DNA replication require a primer?

DNA polymerases can't create a new chain of nucleotides from scratch; they need a pre-existing 3'-OH group to add nucleotides to.


Define replication fork.

The site on the chromosome where DNA replication occurs, and where the enzymes replicating the DNA are bound to untwisted, single-stranded DNA.


Define DNA helicase.

An enzyme that unwinds the double helix, using energy from ATP, to expose a short single-stranded region of DNA for replication.


How do DNA helicase and DNA gyrase work together during DNA replication?

DNA helicase generates positive supercoils ahead of the replication fork as it unwinds the double helix; DNA gyrase moves along ahead of the fork and inserts negative supercoils to counteract the positive ones.


Define origin of replication (oriC).

A single location on the bacterial chromosome where DNA synthesis is initiated.


Define leading strand.

The new strand of DNA synthesized continuously during DNA replication.


Define lagging strand.

The new strand of DNA synthesized in short chunks (Okazaki fragments) during DNA replication, then joined together later.


What allows E. coli to replicate in 20 minutes, given its genome takes 40 minutes to replicate?

Multiple replication forks.


What is MreB?

A protein that forms a simple helical cytoskeleton in bacteria (and some archaea) of long filaments around the inside of the cell, just below the cytoplasmic membrane.


How does MreB define bacterial cell shape?

MreB helices rotate within growing cell cytoplasm and coordinate with cell wall growth proteins to synthesize peptidoglycan where the MreB helices are in contact with the cytoplasmic membrane.


What is bactoprenol?

A lipid carrier molecule that transports peptidoglycan precursors across the cytoplasmic membrane by making them hydrophobic enough to pass through the membrane interior; allows insertion of newly synthesized peptidoglycan into cell wall during growth.


What are transglycosylases?

Enzymes that interact with bactoprenol (carriers) to insert peptidoglycan precursors into the growing point of the cell wall and catalyze glycosidic bond formation.


What are autolysins?

Enzymes that make small gaps in the existing peptidoglycan of the cell wall for insertion of newly synthesized peptidoglycan during cell growth.


Define transpeptidation.

The formation of peptide cross-links between the peptides in peptidoglycan to strengthen the cell wall. 


Penicillin targets transpeptidases. How does this kill bacterial cells?

Transpeptidases catalyze the formation of cross-links between peptidoglycan units within the cell wall; if this process is inhibited, the peptidoglycan is weakened, and the cell eventually bursts.


How do haploid yeast cells reproduce?

Hormones of 1 mating type bind to a cell of the opposite type and change the cell surface so that the 2 cells can fuse to mate and produce a diploid zygote; the zygote can reproduce by budding or undergo meiosis to form ascospores, which germinate to become haploid cells.


Why are yeast cells powerful genetic tools?

In diploid form, they can regenerate cells indefinitely; in haploid form, their genomes are very easy to manipulate.


Define division rate.

The reciprocal of generation time, i.e. the number of divisions (population doublings) in a unit of time.


What are the 4 phases of microbial growth?

  1. Lag phase (little growth as cells adjust to culture)
  2. Exponential phase (maximal cell growth)
  3. Stationary phase (# replicating = # dying)
  4. Death phase (# dying > # replicating)


What are the 3 possible pathways of cell growth leading from starvation/growth arrest?

  • Death phase: most cells starve to death, but robust survivors survive (but can't replicate)
  • Programmed sterility: surviving cells form dormant spores and resuscitate/replicate on change in environment
  • Programmed cell death: some cells activate suicide systems, and surviving cells eat nutrients from dead cells


What happens to the stationary phase of a microbial population if there is a greater number of cells to begin with?

The stationary phase begins earlier, i.e. it takes less time for the number of cells replicating to equal the number of cells dying.


In a continuous culture, what is the effect of increased nutrient concentration?

Greater population growth (to a point).


In a continuous culture, what is the effect of increased dilution?

Increased growth, to a point: too much dilution can flush out cells, halting growth.


Which is more accurate: direct or indirect counting methods?



What happens to cell count estimates by optical density (spectrophotometry) at high cell concentration? Why?

The estimate is too low: counting is based on light scattering, and if there are too many cells, the light will rebound off multiple cells before hitting the detector, so any cells along the way won't be counted.


Define osmotolerant.

Able to grow over wide ranges of water activity or osmotic concentration.


Define halophile.

Requires high levels of NaCl to grow (usually above 0.2 M).


What concentration of NaCl does a halophile need for growth?

At least ~0.2 M.


Define acidophile.

An organism with optimal growth between pH 0 and 5.5.


Define neutrophile.

An organism with optimal growth between pH 5.5 and 8.0.


Define alkaliphile.

An organism with optimal growth between pH 8.0 and 11.5.


Define psychrophile.

An organism that can grow at 0 °C, with optimum growth at 15 °C or lower.


What temperature range results in optimal growth of psychrophiles?

15 °C or lower.


Define psychrotroph.

An organism that can grow between 0 and 7 °C, with optimum growth between 20 and 30 °C (maxed out at 35 °C).


What temperature range results in optimum growth of psychrotrophs?

20 to 30 °C (though they can grow at 0 °C).


What is the maximum temperature at which psychrotrophs can typically grow? 

35 °C.


Define mesophile.

An organism with optimum growth between 20 and 45 °C.


Define thermophile.

An organism that can grow at 55 °C or higher, with optimum growth between 55 and 65 °C.


What temperature range results in optimum growth of thermophiles?

55 to 65 °C.


Define hyperthermophile.

An organism with optimum growth between 85 and ~113 °C.


Define obligate aerobe.

An organism that is completely dependent on atmospheric oxygen for growth.


What is the typical atmospheric oxygen concentration?



Define facultative aerobe/anaerobe.

An organism that does not require oxygen for growth, but grows better in its presence.


Define aerotolerant anaerobe.

An organism that grows equally well in the presence or absence of oxygen.


Define obligate anaerobe.

An organism that does not tolerate oxygen and will die in its presence.


Define microaerophile.

An organism that requires very small concentrations of oxygen to grow (2-10%), and will be damaged by atmospheric concentrations (20%).


Define plezophile (barophile).

An organism with more rapid growth under high hydrostatic pressure.


Define cardinal temperatures.

The minimum, optimum, and maximum temperatures for a particular organism's cell growth.


What is the effect of increasing temperature on microbial growth rates?

Below maximum temperature, temperature increase results in faster enzymatic activity and thus a faster growth rate; catalysis rate doubles every ~10°C. Past maximum temperature, proteins denature and growth drops off.


What happens to cells below their minimum temperature?

Membrane gelling causes transport processes to be too slow for growth.


What happens to cells above their maximum temperature?

  • Proteins denature, so metabolic and growth processes stop
  • Cytoplasmic membrane collapses
  • Eventually: thermal lysis (cell death)


What is the lowest temperature at which viable psychrophilic bacteria have been observed?

Around -12 °C.


What group of organisms makes up the majority of psychrophiles?

Marine microbes.


What temperature class do human pathogens belong to?

Mesophiles (optimal growth between 35 and 40 °C; human body temp. 37.5 °C).


What classes of organisms can be thermophilic?

Usually archaea, with some protists, fungi, and eukaryotes.


What classes of organisms can be hyperthermophilic?

Archaea only.


What are the 2 major types of adaptations found in psychrophilic or psychotrophic microorganisms?

Membrane flexibility and ice crystal prevention.


Define biocide.

Anything that inactivates microbes.


Define sterilization.

Killing all cells, spores, and acellular entities; the highest level of cleanliness.


Define disinfection.

Killing off anything that might cause disease; endospores may survive.


Define sanitization.

An acceptable level of cleanliness determined by public health standards; kills most infectious agents.


Define contamination.

Making a non-living surface safe to handle.


Define antiseptic.

Killing infectious agents on living tissues.


Define chemotherapy.

Killing infectious agents within living tissues.


What word is used to describe a plated colony when no light passes through it?



What word is used to describe a plated colony when light can pass through it?



What does it mean if a plated bacterial colony is opaque?

No light passes through it.


What does it mean if a plated bacterial colony is translucent?

Light can pass through it.


What 2 descriptions are necessary when listing the optical characteristics of a plated bacterial colony?

  1. Whether colonies are opaque (no light passes through) or translucent (light can pass through); and
  2. Whether colonies are shiny (glossy) or dull (matte).


What are the 3 possible descriptors for bacterial colony texture/consistency?

  • Moist: butter-like, easily scooped up
  • Mucoid: slimy/goopy
  • Dry: crumbly, falling apart


What does it mean if a plated bacterial colony is described as being moist?

It has a butter-like texture, easily scooped up.


What does it mean if a plated bacterial colony is described as being mucoid?

It has a slimy, goopy consistency.


What does it mean if a plated bacterial colony is described as being dry?

It has a crumbly texture and readily falls apart.


What are the 2 possible descriptors of water emulsifiability for a plated bacterial colony?

  • Easy: forms a cloudy emulsion
  • Difficult: aggregates/forms clumps


For a plated bacterial colony, when are texture/consistency and emulsifiability typically evaluated?

When cells are transferred from the colony to a slide for Gram staining.


When can odor be evaluated for a plated bacterial colony?

Only when a pure culture has been isolated.


Why is Pseudomonas putida incubated at 30 ºC rather than 37 ºC? 

P. putida is a non-pathogenic species typically found in soil or water, so it prefers temperatures that are lower than body temperature.


What does Pseudomonas putida look like on a TSA plate?

  • Shape: punctiform (<1 mm)
  • Edge: smooth
  • Elevation: convex
  • Colour: white
  • Optical: shiny, opaque


What does Staphylococcus epidermidis look like on a TSA plate?

  • Shape: circular (2-3 mm)
  • Edge: smooth
  • Elevation: convex
  • Colour: cream
  • Optical: shiny, translucent


How can you tell the difference between P. putida and S. epidermidis growing on a TSA plate?

  • P. putida forms punctiform colonies; S. epidermidis forms larger circular colonies
  • P. putida is bright white; S. epidermidis is cream-coloured
  • P. putida colonies are opaque; S. epidermidis colonies are translucent


When preparing a quadrant streak plate, when should you flame the loop?

  • All colonies > 1mm: only after streaking the first quadrant (Q1).
  • Colonies <1 mm: after Q1 and after Q2.


What are the steps of Gram staining?

  1. Crystal violet (60 s)
  2. Water rinse
  3. Gram's iodine (60 s)
  4. Water rinse
  5. Acetone-alcohol (super fast)
  6. Water rinse
  7. Safranin (60 s)
  8. Water rinse


What is the statistically significant range for colony counts on a spread plate?

30 to 300 colonies.


What is the effect of a crowded plate (>300 colonies) on cfu/mL estimates?

Crowding leads to underestimation: colony-forming units may fuse or grow on top of each other, and individual colonies may arise from multiple parent cells.


To what dilution must a cell culture be diluted to ensure an accurate, statistically relevant cell/mL count?

10-6 to 10-7, for 300 to 3000 cells/mL.


In plated cultures, what is a run-on colony?

A colony that forms when daughter cells spread out in a drop of liquid to form a series of connected colonies, which do not have definite divisions between them; counted as a single colony.


When counting plated bacterial colonies, how are run-on colonies counted?

As one colony: there is no way to determine whether it is due to the growth of one original parent cell or from multiple parent cells; multiple daughter cells may have spread out in liquid and established individual colonies where there otherwise would have been only one.


To how many significant figures is cfu/mL reported?



How do you report cfu/mL from TSA spread plates if all plates have >300 colonies?

Estimate the number of colonies from the plate with the highest dilution and lowest volume, and use this count for the calculation; if truly impossible to count, report final count as >300 and use that in calculations.


How do you report cfu/mL from TSA spread plates if all plates have <30 colonies?

Count all plates, keep the count from the plate with the lowest dilution and highest volume for calculations, and report the final value as an estimate.


What is the purpose of the phenyl red (PR) broth test?

To test whether bacteria can ferment a test carbohydrate: acidic end products of fermenation result in a pH change, turning the red medium yellow.