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Flashcards in Chapter 2 Deck (75)

How does a Bright-Field microscope work

Specimens are visualized because of differences in contrast (optical density) between specimen and surroundings


Which two sets of lenses form the image

The objective and ocular lens


What is total magnification

(Objective magnification) x (Ocular magnification)


What is the light source of a miroscope

At the bottom of the microscope, provides a way of illuminating your sample


What is the condenser of a microscope

Focuses the light from the light source onto the sample


What is the stage of a microscope

Used to move the sample around


What is the typical magnification of the eye piece?



What is resolution

The ability to distinguish two adjacent objects as separate and distinct. It determines useful magnification limit


How is resolution determined

Resolution is determined by the wavelength of light used an numerical aperture lens


What is the typical limit of resolution for a light microscope

0.2 um


How big are bacterial cells on average

Often around 1 to 5 um


How big are viruses on average

Often 0.02 um to 0.3 um, so they are too small to be resolved in light microscopes


What happens when you improve contrast

Results in a better final image


How do you improve contrast

By staining, many bacterial cells lack pigments and are very pale


What do you use to stain bacterial cells

Dyes-inorganic compounds that bind to specific cellular materials (methylene blue, safranin, and crystal violet). Most staining procedures kill cells :(


How do you stain a cell

1. Prepare a smear by spreading a culture on a slide, then letting it air dry
2. Pass the slide through the flame to heat fix it
3. Flood slide with stain, rinse and dry
4. Look at it under a microscope


What are differential stains

Used to separate bacteria into groups (gram stain)


What are gram stains widely used in bacteriolology

Bacteria can be divided into two major groups: Gram + and Gram -. Gram + appear purple and Gram - appear red


What is the gram stain procedure

1. Flood the heat fixed smear with crystal violet (all the cells are purple)
2. Add iodine solution (all cells remain purple)
3. Decolorize with alcohol (Gram + cells are purple, Gram - cells are colorless)
4. Counterstain with safranin (Gram + cells are purple and Gram - cells are pink/red)


What is phase-contrast microscopy

It optically produces contrast, phase rings in light path amplify differences in the refractive index of cell and surroundings. Resulting image is DARK cells on a LIGHT background


What is the advantage of phase-contrast microscopy

Improves the contrast of a sample without the USE of a stain, allows the visualization of LIVE samples.


What is dark-field microscopy

The light reaches the specimen from the sides, the light reaching the lens has been scattered by the specimen, the image appears LIGHT on a DARK background. Good for observing the motility of cells


What is fluorescence microscopy

Use to visualize specimens that fluoresce (emit light of one color when illuminated with shorter wavelength) and cells that autofluorescence (chlorophyll in cyanobacteria. Can be used to see subcellular parts of a cells that are normally too small to see


What is a fluorescent dye used on cells

Cells can be stained with a fluorescent dye such as DAPI, which stains DNA. DAPI does not kill cells, can be used to visualize living cells and see where in the cell DNA is.


What is differential interference contrast (DIC) microscopy

Improves contrast and produces high-quality image, uses a polarizer and prism to create two distinct beams of polarized light. Gives structures such as endospores, vacuoles, and granules a 3D appearance


What is atomic force microscopy (AFM)

A tiny stylus is placed close to a specimen and scanned over it's surface to measure weak repulsive forces between it and the specimen's surface. A computer generates an image based on the data from the stylus and can be used to image samples from live whole cells down to isolated proteins bound to DNA, can achieve almost atomic resolution


What is confocal scanning laser microscopy (CSLM)

Uses computerized microscope coupled with laser source to generate a 3D fluorescence image, computer can focus the laser on single optical layers of the specimen (top, middle, bottom). The different layers can then be compiled to produce a 3D image


What is electron microscopy

Uses electrons instead of light (photons) to image cells and structures


What are the 2 types of electron microscopy

Transmission Electron Microscopes (TEM) and Scanning Electron Microscopes (SEM)


What is Transmission Electron Microscopy

Electromagnets function as lenses. The system operates in a vacuum (cells must be dehydrated, fixed, and stained so killed). Has a high magnification and resolution of 0.2 nm. Allows the visualization of structures inside cells at the molecular level. Specimens must be thing and stained with heavy metals


What is Scanning Electron Microscopy

Specimen is coated with a thin film of heavy metal (kills cells) and an electron beam scans the object's surface. The scattered electrons are collected by a detector and an image is produced


What do ALL cells have in common

A cytoplasmic membrane, cytoplasm containing metabolites, enzymes, ribosomes and tRNA for translation, and a DNA genome


Describe a Eukaryotic cell

DNA genome enclosed in a membrane-bound complex, cells are generally larger and more complex than prokaryotes, and contain membrane-obound organelles


Describe a Prokaryotic cell

No membrane-enclosed organelles, no nucleus, and generally smaller than eukaryotic cells


In a prokaryote what is a nucleoid

Region of DNA bound with proteins in a prokaryote, there is no membrane surrounding it like a nucleus in a eukaryote


What are viruses

They are not cells, often just DNA (or RNA) genome associated with a protein coat. They have no metabolic activities on their own and rely completely on biosynthetic machinery of infected host cell (obligate parasites). All types of cells are infected by viruses and smallest virus is only 10 nm in diameter


What is a genome

A cell's full complement of genes


What is a chromosome

An organized structure of DNA and proteins in cells. In prokaryotes they are circular and in humans they are linear


What are plasmids

Prokaryotes also may have small amounts of extra-chromosomal DNA (circular) called plasmids that confer special properties (antibiotic resistance)


What is evolution

The process of genetic change over time that results in new varieties and species of organisms. A result of reproduction, genetics, and ecology.


What evolves over time

Populations evolve over time, not individual cells or organisms


What is phylogeny

Evolutionary (genetic) relationships between organisms. Relationships can be deduced by comparing genetic information in different specimens


What is useful for determining phylogeny

rRNA sequences are good for determining phylogeny because ALL organisms have rRNA


How can you tell if two organisms are evolutionary closely related

If there are less evolutionary differences between the organisms then they may be closer evolutionary related


What are the 3 distinct lineage of cells

Bacteria (prokaryotic), Archaea (prokarytic) and Eukarya (eukaryotic). Archaea and Bacteria are NOT closely related even though they are both prokaryotes, Archaea is more closely related to Eukarya than Bacteria


What do mitochondria and chlororplasts have in common

They contain their own genomes and ribosomes. These organelles are related to a specific lineage of Bacteria. The ancestors of mitochondria and chloroplasts took up residence in Eukarya eons ago


What is endosymbiosis

When the mitochondria and chloroplasts started living in Eukarya and they both benefited from one another


Where do Archaea tend to live

They tend to live in extreme environments


What are chemoorganotrophs

Humans. Obtain their energy from the oxidation of organic molecules/chemicals


What are aerobes

They use oxygen to obtain energy


What are anaerobes

They obtain energy in the absence of oxygen


What are chemolithotrophs

Obtain their energy from the oxidation of inorganic molecules/chemicals (litho=rock,mineral)


What are phtotrophs

Contain organic pigments that allow them to use light as an energy source and can perform oxygenic or anoxygenic photosynthesis


What is oxygenic photosynthesis

Produces oxygen as a byproduct of splitting water to obtain electrons. Electrons are needed to reduce CO2 and make organic sugars. Done by plant chloroplast and cyanobacteria


What is anoxygenic photosynthesis

Does not produce oxygen, electrons come from other molecules other than water (H2S). Performed by green sulfur bacteria


What do all cells require as a major nutrient



What are Autotrophs

Use CO2 as their carbon source (carbon fixation) and are referred to as primary producers


What are Heterotrophs

Require one or more organic molecules for their carbon source (sugars, proteins fats) and they feed directly on autotrophs or live off products produced by autotrophs


What are extremophiles

Organisms that inhabit extreme environments are extremeophiles. Boiling hot springs, glaciers, extremely salty bodies of water. They can't grow in "normal" conditions because their enzymes won't be able to function


What is the domain of all known pathogenic prokaryotes



What makes up the largest phylum of bacteria

Proteobacteria - they are Gram - (E. Coli, Pseudomonas, and Salmonella)


Whats another large group of bacteria but not the largest

Gram + (Bacillus, Clostridium, and Streptomyces)


What are cyanobacteria relatives of

They are relatives of Gram + bacteria but have a Gram - cell wall


What is the Deinococcus phyla of bacteria

They are extremely resistant to radioactivity, can survive dessication, and have a DNA repair process to fix DNA


What is the Chlamydia phyla of bacteria

They are obligate intracellular parasites and can cause disease (STD), will only grow in associated with other organisms


The domain Archaea contains which 2 Phyla

Euryachaeota and Crenarchaeota


What are the Euryachaeota

They contain methanogens, extremehalophiles and thermoacidophiles


What are methanogens

Degrade organic matter anaerobically to produce methan


What are extremehalophiles

Require high salt concentrations for metabolism and reproduction


What are thermoacidophiles

Grow in moderately high temperatures and low pH (acidic) environments


What are the Crenarchaeota

A vast majority of them are hypderthermophiles - organisms that grow at extremely high temperatures


What is metagenomics

A process of isolating DNA from organisms you want, sequencing the DNA of the rRNA and comparing them to a database full of other sequences DNA


What are Spirochetes

They cause syphillis and lyme disease


What are Eukaryotic macroorganisms

Animals, plants, and fungi


What are Eukaryotic microorganisms

Protists (algaea and protozoa), fungi, and slime molds