MBIO 3401 Exam 1

What developed the first method of DNA sequencing fast enough to sequence large genomes?

Fred Sanger.

What is Florence Nightingale famous for?

Florence Nightingale was the first to recognize the significance of disease in warfare. She founded the science of medical statistics and devised the polar area chart to show that the deaths of soldiers was due to various causes.

What is Robert Hooke famous for?

Built the first compound microscope.

Coined the term "cell".

Published the first manuscript that illustrated objects under the microscope.

What is Antonie Van Leeuwenhoek famous for?

First to observe single-cell microbes moving around. He observed samples from his mouth under the microscope, saw them moving around and called them small animals.

He built the first primitive microscope with the intention to observe fine fabrics (he was a cloth draper).

Who discovered the microbial basis of fermentation? How did this person do this?

Louis Pasteur. He built a swan-neck flask and showed that after boiling, the contents remain free of microbial growth despite access to air.

What scientists disproved the theory of spontaneous generation of microbes?

Francesco Redi: showed that maggots in decaying meat were the offspring of flies.

Lazzaro Spallanzani: showed that a sealed flask of meat broth sterilized by boiling failed to grow microbes.

Louis Pasteur: showed that after boiling, the contents in the swan neck flask remain free of microbial growth.

Who is considered the Founding Father of Microbiology?

Louis Pasteur.

What is the Germ Theory of Disease?

That many diseases are caused by microbes (most infectious diseases).

Who is the founder of the scientific method of microbiology?

Robert Koch.

What is the purpose of Koch's Postulates?

Koch's Postulates are a series of criteria (scientific method) for whether a specific microbe is responsible for a specific disease.

List Koch's Postulates in order for defining the causative agent of a disease.

1. The microbe is found in call cases of the disease, but is absent from health individuals.

2. The microbe is isolated from the diseased host and grown in pure culture.

3. When the microbe is introduced into a healthy host, the same disease occurs.

4. The same strain of microbe is obtained from the newly diseased host.

What is a microbe? How small does an organism have to be to be considered a microbe?

A microbe is a living organism that requires a microscope to be seen. Microbe diameter must be less than 0.15 mm.

True or false: Some microbes can consist of a single cell.

True.

A _____ is the total genetic information contained in an organism's chromosomal DNA.

Genome.

What is a collection of sequences taken directly from the environment called?

A metagenome.

Ture or false: Each microbe has the capacity to reproduce its own kind.

True.

What is a cell community?

Many of the same kind of cell.

Should plant and animal cells be considered microbes?

No. Plant and animal cells cannot reproduce their own kind indefinitely. Additionally, animal cells are differentiated and do not exist as independently or as communities.

What types of organisms are considered microbes?

Bacteria, Archaea, Algae, Fungi, protists, and Viruses.

What 14th century disease was caused by microbes?

bubonic plague.

Who was the first scientist to develop the first vaccine based on attenuated strains? What two vaccinations did he develop?

Louis Pasteur. He developed Fowl Cholera vaccination and Rabies vaccination.

Define immunization

The stimulation of an immune response by deliberate inoculation with an attenuated pathogen.

Who discovered that Penicillium mold generated a substance that kills bacteria?

Alexander Fleming.

Who purified penicillin and made it the first commercial antibiotic to save human lives?

Howard Florey and Ernst Chain.

Who first used solid medium using agar to grow pure cultures of microbes?

Angelina and Walther Hesse.

How does the human eye observe images?

Light focuses onto retina where photoreceptor cells fire signals that are transmitted to optic nerve to the brain to generate images.

Define Resolution.

The smallest distance by which two opbjects can be separated and distinguished.

What is the resolution of the human retina? What does this mean?

150 micrometers, or, 0.15 mm.

This means that if two objects are closer than 150 micrometers together, the human eye cannot distinguish between the two objects.

Who was Ignaz Semmelweis?

Semmelweis ordered doctors to wash their hands with chlorine. He was the first to introduce aseptic techniques in the hospitals.

Who was Joseph Lister?

He developed carbolic acid to treat wounds and clean surgical instruments in 1865.

What type of microscopy generates a dark image over a light background?

Bright-field microscopy.

How do you find total magnification?

magnification of ocular multiplied by that of the objective.

Example: ocular = 10x and objective = 20x. Total magnification = 200x.

How do resolution and magnification work together to produce a clear image under microscope?

Increase of magnification results in larger image and increase in resolution produces a clearer image.

True or false: less than 0.1% of all microbial species can be cultured in the laboratory.

True.

What is the wavelength of visible light?

400-750 nm.

Absorption.

Means that the photon's energy is acquired by the absorbing object.

Reflection.

Means that the wavefront bounces off the surface of an object.

Refraction.

The bending of light as it enters a substance that slows its speed.

Scattering.

Occurs when the wavefront interacts with an object smaller than the wavelength of light.

How can we increase resolution when using Bright-Field Microscopy? (5 ways).

1. Use shorter wavelength light.

2. Lessen the contrast.

3. Use immersion oil.

4. Use wider lens closer to specimen.

5. Higher numerical aperture.

What kind of microscope is a system of multiple lenses designed to correct or compensate for aberration?

Compound microscope. Uses ocular lens, objective lens, and needs to be parfocal.

How are wavelength and resolution related?

The shorter the wavelength, the higher the resolution.

What is white light?

a mixture of different wavelengths.

What is polarized light?

A single wavelength.

How are cells detected via fixation and staining?

Fixation is a process in which cells are made to adhere to a slide in a fixed position.

Staining is a process in which cells are given a distinct color. Most stains have conjugated double bonds or aromatic rings, and one or more positive charges.

What is a simple stain?

Adds a dark color to cells.

What is a differential stain?

Stains one kind of cell but not others.

List the steps and purposes of Gram Staining

1. Add methanol to fix cells to surface.

2. Add crystal violet stain and let sit for one minute. This stains cells reversibly.

3. Add iodine. Iodine creates a complex with the crystal violet in gram positive cells that increases stain retention. In gram negative cells, the stain is not retained.

4. Wash with ethanol. This removes color from gram negative cells.

5. Add safranin. Gram positive cells remain purple and gram negative cells are counterstained pink by the safranin.

Differential stain that uses carbolfuchsin to stain the gram positive Mycobacterium species.

Acid-fast stain.

Differential stain that uses malachite green used to detect spores of Bacillus and Clostridium species.

Spore Stain.

Differential stain that colors the background in order to make capsules more visible.

Negative Stain.

What are the advantages of wet mount preparation for observing microbes?

You can see microorganisms in their natural environment.

What are the disadvantages of wet mount preparation for observing microbes?

The mount can dry out easily.

What are the advantages for stained preparations?

You can see the details of the microorganism and it can be used to distinguish one bacterium from another.

What are the disadvantages of stained preparations?

They take more work and is longer to do. You have to use more reagents and the microbes being observed are dead.

What are the disadvantages of wet mount preparation for observing microbes?

The mount can dry out easily.

What is Dark-Field Microscopy? What is dark-field microscopy particularly useful for?

Dark-field optics enables microbes to be seen as halos of bright light against dark background.

Light shines at oblique angle.

Useful to see objects below resolution limit, such as flagella and very thin bacteria. The movement of these objects can be seen to using dark-field microscopy.

Which type of microscopy superimposes refracted light and transmitted light shifted out of phase?

Phase-Contrast microscopy. It can be used to view live cells and cellular organelles.

What type of microscopy is good for viewing larger eukaryotic cells?

Phase-contrast microscopy.

What type of microscopy is used to view marine and pathogenic bacteria?

Fluorescent microscopy.

In which type of microscopy does the specimen absorb light of the excitation wavelength, and then emits light of a lower energy?

Fluorescent microscopy.

True or false: Excitation wavelength is always shorter than emission wavelength.

True.

What is a fluorescent chemical compound called?

A fluorophore.

What is confocal microscopy?

Both excitation light and emitted light are focused together. You take many images of section of different views/planes and feed these sections into a computer that generates a three dimensional image.

What is an advantage of confocal microscopy?

It allows for better resolution and you can visualize cells in three dimensions.

What are the pros of bright-field microscopy?

simple, straight-forward preparation and set up. Very versatile.

What are the cons of bright-field microscopy?

If you want to look at live cells, they are either too small, too pale, and doesn't give you enough contrast.

What are the pros of Dark-field microscopy?

It's good to see very small and very thin microbes, such as flagella.

What are the cons of dark-field microscopy?

You can't see organelles with this type of microscopy. And it is very susceptible to dust contamination.

What are the pros of Phase Contrast microscopy?

This type of microscopy is good to see larger, eukaryotic cells and good for viewing live cells that you can't fix or stain. It can enhance refractive index between media and cells.

What are the cons of Phase Contrast microscopy?

It is difficult to do with small cells and bacteria. You can't see fine structures such as nucleus, cell wall, mitochondria, etc.

What are the pros of fluorescence microscopy?

It can do everything that all other microscopes can do plus fluorescence.

What are the cons of fluorescence microscopy?

It's very expensive.

What type of microscopy is good for viewing internal structures?

Transmission electron microscopy.

What type of microscopy is good for viewing the external features in 3-D?

Scanning electron microscopy.

What are the ways in which a specimen for electron microscopy can be prepared?

1. Embedded in a polymer for thin sections and cut into slices.

2. Treated with a heavy metal salt such as

In which kind of electron microscopy is the specimen flash frozen?

Cryo Electron microscopy.

What kind of microscopy is good for generating high-resolution models of virus particles?

Cryo electron microscopy.

What kind of microscopy enables nanoscale observation of cell surfaces?

Scanning probe microscopy.

What is the structure that defines the existence of a cell?

Cell membrane.

What two components make up the cell membrane? Which component is the more functional part of the membrane?

Lipids and proteins.

Proteins are the more functional part of the membrane.

What role do proteins play in the cell membrane?

1. Structural support.

2. Detection of environmental signal.

3. Secretion of virulence factors and communication signals.

4. Ion transport and energy storage.

What are some unique aspects of the archaea membrane lipid?

They have Ether lipids in the phospholipid side-chain structure that makes them more stable in extreme conditions.

Cyclopentane rings increase stability in extreme conditions.

What fundamental traits do most bacteria share?

1. Thick, complex outer envelope.

2. Compact genome.

3. Tightly coordinated cell functions.

True or false: all bacteria have a cell wall.

False. Not all bacteria have a cell wall.

How does penicillin work?

Penicillin inhibits transpeptidase that cross-links the peptides in the peptidoglycan cell wall of gram positive bacteria.

How does Vanvomycin work?

Vancomycin prevents cross-bridge formation by binding to the terminal D-Ala-D-Ala dipeptide of the peptidoglycan cell wall of gram positive bacteria.

This acid is present in gram positive bacteria and they attach the layers of peptidoglycan together.

teichoic acids.

What is the difference between the cell wall of a gram positive species and a gram negative species?

Gram negative species do not have teichoic acids and they have an inner and and outer membrane that can be seen under microscope.

Why is the minimal size of microbial cells about 0.2 micrometers in diameter?

The number of molecules needed to make a functional cell requires at least a cell size of 0.2 micrometers.

In general, is it easier to develop antibiotics against gram positive or gram negative bacteria?

Gram positive bacteria. This is because gram neg bacteria have two membranes that the antibiotic must cross.

What are the components of the peptidoglycan cell wall?

N-acetylglucosamine, N-acetylmuramic acid, peptides, amino acids.

What is the S-layer?

an additional protective layer commonly found in free-living bacteria and archaea.

Crystalline layer of thick subunits consisting of protein or glycoprotein.

What cellular structure is made of polysaccharides and glycoprotein and protects cells from phagocytosis?

The capsule

What lipids and sugars are specifically found in M. Tuberculosis and M. Leprae?

mycolic acids and arabinogalactans.

What is the inward-facing leaflet of the gram negative outer membrane composed of? What's its purpose?

Composed of lipoprotein. It anchors the outer membrane to the peptidoglycan.

What is the outward-facing leaflet of the gram negative outer membrane composed of? What's its function?

Composed of lipopolysaccharides. It protects against pathogens. It is more porous than the inward facing membrane.

What are the shape-determining proteins of the bacterial cytoskeleton?

FtsZ: forms a z-ring in cocci cells; where cytokinesis occurs. Pretty much all cells have FtsZ.

MreB: forms a coil inside bacilli cells; combination of FtsZ and MreB make the rod shape of bacillus cells.

A lot of bacteria have MreB.

CreS "crescentin": Forms a polymer along the inner side of crescent-shaped bacteria. Less common structural protein.

Cells that have CreS also have FtsZ and MreB proteins.

For what reason might a bacterial cell divide asymmetrically?

Change in environment may make it beneficial to produce one stationary daughter cell and one mobile daughter cell.

Extensively folded intracellular membranes that are the site of conversion of sunlight into energy.

Thylakoid.