Chapter 10: Classification of Microorganisms

Question 1

What is Taxonomy?

Answer 1

Putting organisms into categories.

Kingdom
Phylum
Class
Order
Family
Genus
Species

Question 2

What is phylogeny?

Answer 2

the evolutionary history of a group of organisms, especially as depicted in a family tree.

Question 3

Archaea

Answer 3

. Archaea
Still single celled prokaryotes
Ribosomes different than bacteria
Major categories
Methanogens
Strict anaerobes
Halophiles
Require high concentrations of salt
Hyperthermophiles
Optimal temperatures of close to 100oC

Characteristics reflect those on early Earth

Question 4

Eukarya

Answer 4

Split off from Archaea
Early members still single celled
Single cells more complex than prokaryotes
Eventually differentiated into complex, multicellular organisms

Question 5

What is serology based upon?

Answer 5

the interaction of an antibody and an antigen

Question 6

What is the plate that has all of the media in ine place, and allows you to just streak your bacteria culture across the whole thing?

Answer 6

Enterotube II from Becton Dickinson

Question 7

How does serology work?

Answer 7

Serum antibodies are generated by the immune system in response to a foreign antigen.

The way to tell if an antigen is present is whether or not agglutination happens. If it does this mans that the antibodies have bound the antigen.

Question 8

What is a slide agglutination test?

Answer 8

Known antiserum (housing specific antibodies) is mixed with an unknown culture to test for agglutination.

Antibodies are specific, so positive agglutination helps to identify the culture.

Question 9

What does ELISA stand for?

Answer 9

Enzyme Linked ImmunoSorbent Assay

Question 10

How does ELISA work?

Ps. It’s all about visual detection.

Answer 10

1. Known antibodies are bound to well
2. Patient sample is added to well; complementary antigen binds to antibody.
3. An enzyme linked antibody specific for the test antigen is added. It binds to the antigen.
4. Enzyme substrate is added, and the reaction produces a product that causes visible blue color change.

Question 11

What is ELISA used to detect?

Answer 11

Antigens present in patient

Question 12

What is an over the counter example of ELISA?

Answer 12

A Pregnancy test. HCG is the antigen being detected.

Question 13

What are Western Blots used to identify?

Answer 13

Proteins AKA antibodies in a patient’s serum

Question 14

What is different between a Western and a Southern Blot?

Answer 14

Once the information is picked up from the gel by the filter, it is washed in human serum. That is when certain antigens (proteins run in the gel) will bind to the antibodies in the serum

Question 15

How does Phage Typing work?

Answer 15

A grid is made on an agar plate.

the whole p;late is inoculated by bacteria.

A phage is placed in each box of the grid.

Viruses (bacteriophages) bind to specific receptors on the outside of certain bacteria that have the specific receptors for the phage.

This is significant, because as the bacteria grows overnight, certain phages from the boxes will bind to the receptors and the cell will be lysed, leaving a visual explosion looking mark in the boxes corresponding to certain phages.

From this information, we can begin deducing what the bacteria is.

Question 16

How does DNA base composition work?

Answer 16

Bacteria can be identified by the make up of their base pairs. Tests are tun to llok at the %GC vs %AT

Question 17

What is the Gold Standard for Becterium Classification?

Answer 17

rRNA sequencing

Question 18

why is rRNA sequencing the best candidate?

Answer 18

All organisms have it, , it’s not a hotspot for mutation, it’s easy to sequence, and it is called a clock because it each tick is a new/different mutation.

Question 19

What is DNA Fingerprinting?

Answer 19

Restriction enzymes cut a molecule of DNA everywhere a specific base sequence occurs, producing restriction fragments. This is done to multiple organisms separately.

Then, the fragments are placed into the wells of agarose gel and run through electrophoresis. The result of each well’s electrophoresis is the organism’s DNA fingerprint.

These fingerprints can be compared and show similarities/relations between organisms.

Question 20

How can a bacterium be classified using PCR?

Answer 20

NUCLEIC ACID AMPLIFICATION

When a microbe cannot be cultured by conventional methods, PCR can be used to amplify the DNA. Specific primers for specific microbes can be used to test the identity of the organism.

Question 21

What is the process of Nucleic Acid Hybridization?

Answer 21

1. Heat separates DNA strands
2. Single strands of DNA from each organism are put together in solution.
3. Solution is cooled to allow renaturation of double stranded DNA

**Complete rehybridization=organisms are identical

***Partial Hybridization=organisms are related

**No Hybridization=organisms are unrelated

Question 22

What are DNA Chips?

Answer 22

The DNA chip or microarray can quickly detect a pathogen in a host or the environment by identifying a gene unique to the pathogen.

The chip is composed of DNA probes of known organisms. Hybridization of unknown DNA with known DNA of the chip allows us to figure out what the unknown DNA is.

Question 23

What is FISH?

Answer 23

FLUORESCENT IN SITU HYBRIDIZATION

Fluorescent dye-labeled RNA or DNA probes are used to specifically stain microbes in place (situ).

Cells are treated so that the probe enters the cell and reacts with the target DNA still inside the cell.

Question 24

What is FISH used to determine?

Answer 24

Identity, abundance, and relative activity of microorganisms in an environment.

It can also be used to detect bacteria that have not yet been cultured. As specific probes are developed, FISH can be used to detect bacteria in drinking water or in a patient very quickly, eliminating the time it would take to culture bacteria.