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BI 234 > Lecture One: Intro/History/Microscopy/Taxonomy/Phylogeny > Flashcards

Lecture One: Intro/History/Microscopy/Taxonomy/Phylogeny Flashcards

1
Q

Animalcule

A

“tiny” eggs Antonie van Leeuwenhoek found on rotten mean

Discovered using a simple microscope

Microscopic organisms (archaic term)

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2
Q

Antisepsis

A

The practice of using antiseptics to eliminate the microorganisms that cause disease.

Joseph Lister sprayed carbolic acid (phenol) on surgical wounds and their rate of infection decreased

His work popularized surgical antisepsis to reduce perpetual fever

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3
Q

Archaea (Domain)

A

A type of single-celled organisms

Do not have nuclei or organelles

Differs from Bacteria in that they do not contain peptidoglycan

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4
Q

Brightfield (Microscopy)

[What it is…; Looks like…; Why it is useful…; Good for…]

A

A way of using a compound microscope;

What it is: Basic light microscopy

Looks like: bright background, cells almost invisible, but pigments and stained objects are dark and colored

Why it is useful: it is the least expensive way to see truly tiny objects like bacterial cells.

Good for: observation of stained (dead) specimens
or very pigmented live organisms
(not most bacteria)

Histology, Gram staining, looking at large algae in pond water
magnification = up to 1,000x
resolution = 0.2μm or worse

Inexpensive and easy to use up to 1000X

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5
Q

Broth

A

A liquid medium containing proteins and other nutrients for the culture of bacteria.

Needham used boiled mutton broth to see if animalcules arose from vital force.

Pasteur used boiled broth and found it would only rot if it was exposed to air and/or the trapped dust in the swan neck flask

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6
Q

Cell Theory

[Three major points]

A
  1. All cells come from other cells
  2. Cells are the smallest unit of life
  3. All living organisms are made of cells
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7
Q

Cholera

A

an acute diarrheal illness caused by infection of the intestine with Vibrio cholerae bacteria

John Snow studied the biggest case in London in 1854 (beginning of modern-day epidemiology)

Residents blamed miasma / John Snow found it was fecal matter from infected baby and the source was a local water pump

Authorities refused to believe since it was gross so they stuck with miasma

Pasteur also tried working with it, but could not get pure culture, and did not mean Koch’s postulates

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8
Q

Compound Microscope

A

A microscope used for viewing samples at high magnification (40 - 1000x), which is achieved by the combined effect of two sets of lenses: the ocular lens (in the eyepiece) and the objective lenses (close to the sample).

Use visible light

Existed in the 1600’s but glass manufacturing was lacking

has a resolution of 0.2μm at best

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9
Q

Darkfield (Microscopy)

[What it is…; Looks like…; Why it is useful…; Good for…]

A

A way of using a compound microscope;

What it is: Condenser contains opaque disc that blocks direct light, but allows light reflected from specimen to enter. Specialized objectives must be used.

Looks like: dark background, bright cells

Why it is useful: provides extra contrast even without stains: especially for certain live microorganisms that can’t be seen with brightfield.

Good for: examining unstained, living microorganisms for size, shape, motility

magnification = up to 1,000x
resolution = 0.2μm or worse
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10
Q

Epidemiology

A

The study of disease patterns

The swan-neck flask was the end of believing in “spontaneous generation” but epidemiology was around before the creation of the flask.

Ignaz Semmelweis: Obstetrician at a Vienna General Hospital teaching hospital.

Modern epidemiology began with modern cholera and John Snow

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11
Q

Eukarya / eukaryote (domain)

A

Animals, fungi, and plants are examples

Single cells that have nuclei and organelles are all found in the domain Eukarya

Most “modern” eukaryotes have mitochondria, which share a common ancestor with proteobacteria!

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12
Q

Evolutionary Distance

A

Lines used to measure the distance between two species / specimens.

When using horizonal lines, only count the number of horizonal lines; length does not matter

Length does matter when using phylogenetic trees

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13
Q

Fluorescence (Microscopy)

[What it is…; Looks like…; Why it is useful…; Good for…]

A

A way of using a compound microscope; much more common today in research than any of the others we’ve seen so far

What it is: microscopy where one color of light “excites” molecules (fluorochromes) that emit a different color. Special filters prevent us from seeing the first “excitation” color, so only the second, emitted color is visible. (special proteins have this fluorescence property)

Looks like: dark background, brightly glowing colored spots

Why it is useful: It is very specific: only the special pigments/proteins are visible. Scientists can use this to find very specific structures within cells.

Good for: observation of specimens stained (usually dead but not always) using fluorescent pigments, or transgenically producing fluorescent proteins

magnification = up to 1,000x
resolution = 0.2μm or worse

Very expensive

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14
Q

Fly (insect)

A

Specimens used in Francesco Redi’s experiment on spontaneous generation

Redi believed maggots spawn from adult flies

Maggots only appeared in open containers with meat in them

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15
Q

Germ Theory of Disease

A

States that infectious diseases are caused by microorganisms.

Robert Koch provided great evidence in favor of the Germ Theory of Disease through the injecting of diseased blood into rats

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16
Q

Gram Stain

A

A method of staining used to classify bacterial species into two large groups: Gram-positive and Gram-negative

Gram-positive bacterial cell (thick peptidoglycan) moves from purple to blue-purple when method is complete

Gram-negative bacterial (thin peptidoglycan) cell moves from purple to orange-red when method is complete

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17
Q

Crystal violet (Gram Stain)

A

The first step in the gram stain method

A positive charged dye that adheres to the cell wall of all cells

Turns both gram-positive and gram-negative cells purple

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18
Q

Iodide (Gram Stain)

A

The second step in the gram stain method

Added as a mordant to form the crystal violet-iodine complex so that the dye cannot be removed

Turns both gram-positive and gram-negative cells from purple to blue-purple

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19
Q

Ethanol (Gram Stain)

A

The third step in the gram stain method

Acts as a solvent which causes the crystal violet-iodine complex to dissolve away and rinse out of the cell wall if the cells are gram negative

Ethanol does not wash away the iodide and the cell stays blue-purple and gram-negative cells are washed and loses its blue-purple stain

20
Q

Safranin (Gram Stain)

A

The fourth step in the gram stain method

Used as a counter-stain that directly stains the bacteria that has been decolorized.

Has not effect on gram-positive cells but turns gram-negative cells orange-red

21
Q

Koch’s postulates

A

Set of experimental results that will convince the scientific community that a given microorganism is the main cause of a disease.

The microorganism is both NECESSARY and SUFFICIENT
to cause the disease

  1. “The same microorganisms are always present in every case of the disease.”
  2. “The microorganisms are isolated from the tissues of the ‘diseased lesion’ and are grown in pure culture.“
  3. “Microorganisms from the pure culture, if inoculated into a healthy animal, reproduce the disease.”
  4. “Identical microorganisms are isolated from the new ‘diseased lesion.’”

Created this through is anthrax research

22
Q

Maggot

A

Used in Francesco Redi’s experiments to disprove spontaneous generation

Maggots appeared on the meat that was uncovered

23
Q

Magnification (microscopy)

A

Total magnification = Ocular x Objective

A key aspect of microscopes

24
Q

Miasma (Miasmatic Theory)

A

Theory that specific bad smells or “corrupt air” can cause disease.

Once microorganisms were linked to disease, miasmatic theory suggested that corrupt air could create microorganisms.

Spallanzani improves Needham’s experiment by boiling the broth after the tubes were capped; leading to the possible disproving of Miasmatic Theory

Still held true for London residents because they didn’t want to believe John Snow

25
Q

Mutton Broth

A

Key ingredient in Needham’s experiment of boiling broth to see if animalcules arose from vital force

26
Q

Phase Contrast (Microscopy)

[What it is…; Looks like…; Why it is useful…; Good for…]

A

A way of using a compound microscope; much more common today in research than any of the others we’ve seen so far

What it is: Condenser restricts light to a ring-shaped opening. Together with specialized objectives, helps make visible differences in phase of light. Don’t worry if the previous sentence doesn’t make sense to you.

Looks like: bright background, dark cells, no color. This is because cytosol slows light slightly, putting it out of phase with surrounding light..

Why it is useful: It is the least expensive way to living bacteria. 100X objectives are commonly available.

Good for: observation of unstained (living) specimens. It is more expensive than brightfield so it is not as common. It is more common (and less expensive) than darkfield.

magnification = up to 1,000x
resolution = 0.2μm or worse
27
Q

Phylogeny

A

Is the study of evolutionary relationships between organisms

Taxonomy is based on phylogeny

Murky until the discovery of DNA sequencing

Phylogenies of microorganisms are more difficult to determine and rRNA sequence comparisons

28
Q

Phylogenetic Tree

A

Visual to show the relationships between species

Length of lines indicate closeness of phylogenetic relationships

29
Q

Pure Culture

A

A population of microorganisms that are all of the same type

Key aspect of Koch’s Postulates

Pure Culture was not available to Pasteur and his cholera studies

30
Q

Resolution/ Resolving Power (Microscopy)

A

The ability to discriminate two adjacent objects as separate

Lower resolution = better, more detailed

Human eye has 100µm; compound microscope goes down to .2µm

The main limiting factor for microscopes.

Magnifying does not improve resolution

31
Q

rRNA

A

Ribosomal ribonucleic acid (rRNA)

type of non-coding RNA which is the primary component of ribosomes, essential to all cells.

rRNA is a ribozyme which carries out protein synthesis in ribosomes.

Comparing rRNA helps with microorganism phylogeny

32
Q

Scanning Electron Microscopy (SEM)

[What it is…; Looks like…; Why it is useful…; Good for…]

A

What it is: Thin electron beam scans across a sample that has been coated with a very thin layer of electrically conductive metal.

“Secondary electrons” are emitted where the beam strikes the coating. These are detected by sensitive detectors nearby.
Computers then reconstruct an image that shows depth in addition to height and width.

Looks like: Black and white (or false color) pictures showing 3-dimensional shapes. NOT cross sections.

Why it is useful: It can show depth information, and it has very good resolution.

Good for: Determining the shape of surface features.

magnification = up to 100,000x
resolution = 0.005μm or worse
33
Q

Swan-necked flask

A

Instrument used in Pasteur’s studies

Showed that dust is a major cause of microbial contamination

Dust was trapped in the swan-necked flask

Seen as the end of spontaneous generation

34
Q

Spontaneous Generation (Theory)

A

The idea that living things can arise from non-living things.

Frankenstein’s monster is a good example of this idea

Vital force, Miasma, and Humors are all types of spontaneous generation

35
Q

Taxonomy

A

the systematic classification of organisms into groups

Ideally, taxonomy is based on phylogeny

36
Q

taxonomic level/ taxonomic group

A

Levels used to describe most common ancestors

Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species
37
Q

Domain (Taxonomic Level)

[When was most common ancestor alive; Human; Relative]

A

A taxonomic level

Three groups: Eukarya, Archaea, and Bacteria

Common ancestor lived ~2 billion years ago

Human: Eukarya

Relative: Red Oak

38
Q

Kingdom (Taxonomic Level)

[When was most common ancestor alive; Human; Relative]

A

A taxonomic level

Common ancestor lived between 300 million & ~2 billion years ago

Human: Animalia

Relative: Jellyfish

39
Q

Phylum (Taxonomic Level)

[When was most common ancestor alive; Human; Relative]

A

A taxonomic level

Common ancestor lived between 300 million & ~2 billion years ago

Human: Chordata (Vertebrata)

Relative: Penguin

40
Q

Class (Taxonomic Level)

[When was most common ancestor alive; Human; Relative]

A

A taxonomic level

Common ancestor lived between 300 million years ago

Human: Mammalia

Relative: Platypus

41
Q

Order (Taxonomic Level)

[When was most common ancestor alive; Human; Relative]

A

A taxonomic level

Common ancestor lived between > 2 million & 300 million years ago

Human: Primate

Relative: Howler Monkey

42
Q

Family (Taxonomic Level)

[When was most common ancestor alive; Human; Relative]

A

A taxonomic level

Common ancestor lived between > 2 million years ago

Human: Hominidae

Relative: Orangutan

43
Q

Genus (Taxonomic Level)

[When was most common ancestor alive; Human; Relative]

A

A taxonomic level

Common ancestor lived 2 million years ago

Human: Homo

Relative: “Hobbit”

44
Q

Species (Taxonomic Level)

[When was most common ancestor alive; Human; Relative]

A

A taxonomic level

Common ancestor lived < 2 million years ago

Human: sapien

Relative: ??

45
Q

Transmission Electron Microscopy

[What it is…; Looks like…; Why it is useful…; Good for…]

A

What it is: A thin beam of electrons scans across a very, very thin sample. The sample has been stained with metals that absorb electrons.

Electron-sensitive film on the other side detects electrons that passed through the samples without being absorbed

Looks like: Black and white (or false color), with fine details from cross sections of cells.

Why it is useful: It has the best resolution therefore most useful magnification) of any common form of microscopy.

Good for: Finding the actual shapes or locations of intracellular structures in stained, dead, thinly sliced samples.

magnification = up to 700,000x
resolution = 0.001μm or worse
46
Q

Theory (Scientific)

A

a testable hypothesis that has been tested many times and has never been refuted

47
Q

Universal Phylogenetic Tree

A

A phylogenic tree with a universal ancestor and branches off into bacteria, archaea, and eukarya

BI 234 (4 decks)

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