Microbe Mission Practice

What is the primary function of endospores?

Survival in harsh conditions

What is not a basic structural component of a virus?

Cell membrane

What is a nonspecific defense against pathogens?

Mucus

First section of a bacterial growth curve

lag phase

Second section of a bacterial growth curve

Exponential or log growth

Third section of a bacterial growth curve

stationary phase

Last section of a bacterial growth curve

death or decline

Most common cause of viral gastroenteritis

Norovirus

Disease often spread in healthcare facilities; resistant to most commonly used antibiotics

MRSA

Brain-eating amoeba

Naegleria fowleri

Characteristic of having two nuclei

Giardia

Rickettsia rickettsii

Causes Rocky Mountain Spotted Fever

Mycobacterium leprae

Causes leprosy, aka, Hansen’s disease

Mycobacterium tuberculosis

Causes Tuberculosis

Microcystis aeruginosa

Causes harmful algal blooms

Staphylococcus aureus

causes skin and soft tissue infections

Helicobacter pylori

Causes stomach infections

Pyrococcus furiosus

used in the process of DNA amplification

Methanococcus sp

has the potential for H2 and CO2 based biotechnologies because of its ability to rapidly metabolize H2

Plasmodium falciparum

causes malaria

Saccharomyces cerevisiae

main source of nutritional yeast

nannochloropsis sp

marine microalgae

paramecium sp.

decomposes smaller microbes

capsid

protein coat made of protomers; holds the DNA or RNA in a virus

nucleocapsid

nucleic acid (DNA or RNA) and capsid coat

Three types of capsid symmetry

helical, icosahedral, and complex

helical capsid

shaped like hollow tubes

icosahedral capsid

20 equilateral triangles; most efficient way to close a space

complex capsid

neither icosahedral nor helical

Heat fixation

Typically used to observe prokaryotes; preserves overall morphology, but not inner cell structures

Chemical fixation

used to protect fine cellular substructure and the morphology of larger, more delicate microrganisms; penetrates cells and reacts with proteins and lipids to render them inactive, insoluble, and immobile

gram-positive cell wall

consists of a 20 to 80 nm thick homogenous layer of peptidoglycan

gram-negative cell wall

consists of a 2 to 7 nm peptidoglycan layer and a 7 to 8 nm outer membrane, with periplasmic space in-between

gram-positive cells stain

purple

gram-negative cells stain

pink

bright-field microscopy

Sample illumination is transmitted white light, and contrast in the sample is caused by attenuation of the transmitted light in dense areas of the sample; the simplest of a range of techniques used for illumination of samples in light microscopes, and its simplicity makes it a popular technique. The typical appearance of a bright-field microscopy image is a dark sample on a bright background, hence the name.

dark-field microscopy

exclude the unscattered beam from the image. Consequently, the field around the specimen (i.e., where there is no specimen to scatter the beam) is generally dark.

phase-contrast microscopy

passes diffracted and non-diffracted light through a phase-plate so disrupt caused by the light passing through the cell are clearly visible

vesicles

small, membrane-enclosed sacs that bud off from the membranes of the ER, Golgi body, and plasma membrane. Vesicles carry substances between these cell parts, and play a key role in transporting substances within and out of the cell.

fimbria

Long filamentous polymeric protein structures located at the surface of bacterial cells. They enable the bacteria to bind to specific receptor structures and thereby to colonise specific surfaces. Fimbriae consist of so-called major and minor subunits, which form, in a specific order, the fimbrial structure.

eyespots

The eyespot apparatus (or stigma) is a photoreceptive organelle found in the flagellate or (motile) cells of green algae and other unicellular photosynthetic organisms such as euglenids. It allows the cells to sense light direction and intensity and respond to it, prompting the organism to either swim towards the light (positive phototaxis), or away from it (negative phototaxis).

Fluorescence Microscope

Microscopy based on the principle of removal of incident illumination by selective absorption, whereas light that has been absorbed by the specimen and re-emitted at an altered wavelength is transmitted. The light source must produce a light bean of appropriate wavelength. An excitation filter removes wavelengths that are not effective in exciting the fluorochrome used. The light fluoresced by the specimen fluorescence contributes to the intensity of the image being viewed.

Incident Illumination

Illumination that falls on an object from multiple directions

Transmission Electron Microscopes

specimens are fixed on a support grid and and either embedded in resin or stained with compounds (such as uranyl aceate or osmium tetroxide); regions of the specimen can be electron dense or sparse depending on how much stain they receive; this is used to visualize the image as electron dense regions “take” more energy from the electron beams than electron sparse regions

Sample must be dehydrated, embedded in resin, and cut into ultra-thin slices with diamond knife (they must be this thin so electrons can pass through them); better resolution compared to SEM

Electron Microscopy (general)

precision up to 0.2 nm; magnification up to 1,000,000 x; electron beam (De Broglie) wavelength ~0.01nm

Can’t visualize live specimens; expensive to image; requires extensive training to use

Scanning Electron Microscopy

Specimens are coated with vaporized gold or palladium ions

Primary electrons from the electron beam are used to displace secondary electrons from the sample; these are used by the scanning electron microscope to view the sample

SEM is primarily used to view specimens in terms of crystallography, topography, and magnetic field; worse resolution TEM

Counting Cells using a Neubauer Counting Chamber

1. Cells are detached

2. Dilute the cells (optional, but especially useful for a large quantity of cells

3. Dilution factor refers to how much total volume of the solution is used for 1 unit of the actual cell culture

4. Transfer the solution onto the counter chamber

5. Count the cells per a 1/9 square of the counting chamber (if the cell is touching the lower or right boundary line it counters for the square; if it touches the upper or left boundary line it does not

6. Calculate how many cells per milliliter there are in the counting chamber based on the dimensions of one of the 1/9 square (1 mm x 1 mm x 0.1 mm)

7. Multiply using ratio

Hyphae definition

Branching, thread-like filaments that make up the body of a fungus

A network of hyphae is called a _____

Mycelium

Transpeptidase

Enzymes responsible for the cross-linking of peptidoglycan chains

Penicillun and its family targets what aspect of bacterial cell walls?

Transpeptidase

You find a single cell with a light microscope, that is not mobile, and when you examine it, you see no organelles in the cell. What is it?

Bacterium

Typical characteristics of a mycobacterium tuberculosis colony

Pale yellow color, dry/crumby, wrinkly

Viral DNA can be:

I and III only (single-stranded, double-stranded, or partially double-standed)

Iron-oxidizing bacteria can use iron:

to generate ATP, as a source of energy to fix carbon

What bacterial strain is used in the production of yogurt?

Lactobacillus bulgarius and Strepococcus thermophilus

Agar is used for solidifying culture media because:

It is not affected by the growth of the media, It does not add to the nutritive properties of the medium, the melting and solidifying points of agar solution are not the same

What describes the mechanism by which beta-lactam antibiotics inhibit bacterial growth, and the potential bacterial response to this inhibition

Beta-lactams inhibit transpeptidase enzymes, preventing cross-linking of peptidoglycan, and bacteria may resist by producing beta-lactamases or altering penicillin-binding proteins (PBPs)

A lysogenic virus infects a bacterial cell, incorporating its genetic material into the cell’s genome. What is this process called?

Transduction

The outer membrane of mitochondria and chloroplasts is biochemically similar to the:

Bacterial membrane

Gram positive bacteria have a:

thick cell wall

When is a lag phase necessary?

When cells are old, damage, or need to adapt to a new environment

Confocal Microscope Mechanism

Focusing two different light sources on a subject for better contrast

Some antibiotics that treat ribosomes of infectious bacteria can inhibit protein synthesis in certain organelles of eukaryotic cells. This is evidence for what?

Some organelles within eukaryotic cells are the descendants of free-living prokaryotes

Who was endosymbiotic theory proposed by?

Lynn Margulis

PCR meaning

Polymerase Chain Experiment; used to rapidly re-produce segments of nucleic acid

Microbial Phylogenetics meaning

the study of the evolutionary relatedness among various groups of microorganisms

Why is the 16S rRNA gene commonly used in microbial taxonomy?

It contains conserved and variable regions, helping with phylogenetic comparisons

Are there more microbe on/in the human body than skin cells?

There are more microbes in the human body than skin cells

What best describes the purpose of 16S/18S rRNA amplicon sequencing in microbial ecology?

To assess the taxonomic composition and diversity of microbial communities

Kirby-Bauer Disk Diffusion Method

Qualitatively tests multiple antibiotics at once; fast; cost-effective; easy to interpret

Acid fast staining is used to detect bacteria in the genuses:

Mycobacterium (and Nocardia)

What makes acid-fast bacteria resistant to traditional gram staining?

The high mycolic acid content in their cell walls

What is the role of a contractile vacuole in a freshwater protist?

Remove excess water to maintain osmotic balance

Cyanobacteria

Blue-green algae; photoautotrophs

Which microbes are most commonly biogenetically engineered to become “insulin factories”

bacteria (and archae)

In the study of bacteriophages, what is the significance of restriction modification systems in bacteria?

They protect bacterial cells from phage infections by cutting foreign DNA.

Otherwise noninfectious viruses may be made infectious by what process?

Viral Transduction

Are protozoans eukaryotic or prokaryotic?

Eukaryotic

The enzyme which converts optically active isomers of lactic acid to the optically inactive racemic mixture is which of the following?

Racemase

What could be used as a fixative in transmission electrom microscopy?

Osmium tetroxide

Positively vs. Negatively Supercoiled

Positively supercoiling makes DNA more difficult to unwind; Negatively Supercoiling facilitates DNA unwinding which is necessary for processes such as replication and transcription

Function of carboxysomes in cyanobacteria and proteobacteria

They concentrate carbon dioxide around RuBisCO to enhance photosynthetic efficiency and reduce photorespiration

What is the resolving power of a transmission electron microscope?

0.2 nm

What are the outputs of oxygenic photosynthesis?

Glucose, O2, ATP, NADPH

Specific function of the sigma factor in initiating transcription

It facilitates the recruitment of RNA polymerase to promoter regions by recognizing specific DNA sequences

Pleiomorphic meaning

the ability of a microbe to to alter its shape or size in response to environment conditions

Mesosomes

Invaginations of the plasma membrane found in prokaryotic cells