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MCB2004 > L12: Classification of Microorganisms > Flashcards

L12: Classification of Microorganisms Flashcards

(90 cards)

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1
Q

taxonomy definition

A

the science of classifying organisms by degree of similarities among them

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2
Q

taxonomy nomenclature

A

provides universal names for organisms
provides reference for identifying new organisms

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3
Q

systematics/phylogeny definition

A

study of the evolutionary history of organisms

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4
Q

true or false: bacteria and archaea, the 2 prokaryotes, share many similarities

A

false; bacteria and archaea differ in biochemistry, function, and etc.

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5
Q

true or false: archaea are more similar to eukaryotes than either are similar to bacteria

A

true; see tree of life diagram

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6
Q

endosymbiotic theory

A

eukaryotes came from prokaryotes that mutated and got ingested/infected by other prokaryotes, becoming endosymbionts; first began with bacteria evolving into mitochondria and chloroplasts

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7
Q

what is the evidence for endosymbiotic theory?

A

mitochondria and chloroplasts share similarities w/ bacteria:
- contain 70S ribosomes
- have tiny circles of DNA
- divide via binary fission
- share the first amino acid (Formylmethionine)

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8
Q

phylogenetics pt. 1

A

each species retains some characteristics of its ancestor

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9
Q

phylogenetics pt. 2

A

grouping organisms by common properties implies that a group of organisms from a common ancestor

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10
Q

phylogenetics are based on…

A

anatomy
fossils
rRNA seq similarity

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11
Q

scientific nomenclature

A

is binomial: genus + specific epithet
italicized OR underlined
genus is ALWAYS capitalized
specific epithet is ALWAYS lowercase

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12
Q

taxonomic hierarchy: phylum to species

A

phylum
class
order
family
genus
species

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13
Q

classification definition

A

placing organisms in groups of related species

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14
Q

identification definition

A

matching characteristics of an “unknown” organism to lists of known organisms

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15
Q

prokaryotic species definition

A

a population of cells with similar characteristics

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16
Q

culture

A

a population of bacterial cells grown in laboratory media

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17
Q

clone

A

population of cells derived from a single cell

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18
Q

strain

A

genetically different cells within a clone in which strains are differentiated based on the 16S ribosome

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19
Q

how do strains differ from species?

A

strains are closely related enough to where they are considered the same species, but have some genetic differences

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20
Q

strain example

A

harmless lab E. coli strains vs. E. coli O157:H7

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21
Q

do bacteria have kingdoms?

A

no; bacteria and archaea are domains

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22
Q

in the domain eukarya, what are the 4 kingdoms?

A

animalia
plantae
fungi
protista

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23
Q

animalia traits

A

multicellular
NO cell walls
chemoheterotrophic

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24
Q

plantae traits

A

multicellular
cellulose cell walls
photoautotrophic (mainly)

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25
fungi traits
multi- OR uni-cellular chitin cell walls develop fr. spores, hyphal fragments
26
protista traits
wide variety grouped into clades by rRNA
27
what is special about protists/protozoans?
protista is the "miscellanous" category for eukaryotes that do NOT fit the criteria for the other kingdoms
28
eukaryotic species definition
a group of closely-related organisms that breed among themselves most are diploid or polyploid; most reproduce sexually
29
eukaryotes being diploid or polyploid, and able to reproduce sexually limits interbreeding to...
only eukaryotic organisms that are closely related
30
viral species definition
population of viruses w/ similar characteristics that occupy a particular ecological niche
31
what is special about viral species?
viral species are hard to classify
32
what are the 3 main identification methods?
analyzing morphological characteristics differential staining biochemical tests
33
morphological characteristics
useful for identifying eukaryotes somewhat useful for bacteria and viruses
34
differential staining
includes Gram staining, acid-fast staining useful for identifying bacteria
35
biochemical tests
determines presence of bacterial enzymes
36
what are the identification methods for bacteria?
1. metabolic biochemical tests 2. immunoassays 3. flow cytometry 4. protein profiling by mass spectrometry 5. fatty acid profiling 6. bacteriophage typing 7. DNA methods
37
metabolic biochemical tests
require growing bacteria in a culture from a sample
38
immunoassays
the most common diagnostic test uses antibodies can identify antigens (bacteria) based on what antibodies are produced, etc.
39
flow cytometry
uses differences in electrical conductivity between different types of cells in some cases, are part of immunoassays
40
how does flow cytometry identify microbes?
differential fluorescence in cells; can be produced by staining w/ fluorescent dye that stains some cells but not others fluorescence = signifier of infection
41
how is flow cytometry incorporated into immunoassays?
cells can also be labeled w/ an antibody that selectively binds some cells; the antibody can be attached to a fluorescent dye
42
protein profiling by mass spectrometry
cellular proteins are profiled chemically and compared to known standards for particular bacterial stains
43
fatty acid profiling
AKA fatty acid methyl esters compares differences in FA profiles to standards
44
bacteriophage typing
an older, now less-used method set of phages (viruses) infects a bacterial strain to determine the strain identity
45
phage
viruses that attack bacteria
46
what is the mechanism of phage typing?
some strains of a bacterial species will be sensitive to a particular phage, and others will be resistant
47
how to use phage typing?
know which bacteria are sensitive and which are resistant to a set of well-characterized phage so you can use the phages to identify the bacteria in an unknown sample
48
clear spots signify that...
the strain is extremely sensitive to that phage
49
partially clear spots signify that...
the strain is partially resistant
50
opaque spots signify that...
the strain is completely resistant to that phage
51
DNA methods
- DNA fingerprinting methods - rDNA sequencing - hybridization - whole genome sequencing
52
DNA methods: rDNA sequencing
identifies bacteria via the 16S rDNA gene (ribotyping); is amplified by polymerase chain reaction (PCR)
53
DNA methods: older methods such as ______ and ________ are being phased out
DNA fingerprinting DNA base composition
54
DNA methods: DNA fingerprinting
electrophoresis of restriction enzyme digests
55
DNA methods: DNA base composition
measures % of G + % of C (GC%); bacteria have very low to very high ranges of GC%
56
DNA methods: DNA hybridization
requires a "DNA probe"
57
serological tests (immunoassays)
uses antibodies (AKA immunoglobulins)
58
what are the main types of immunoassays/serological tests?
1. slide agglutination test 2. ELISA (enzyme-linked immunosorbent assay)
59
slide agglutination test
latex beads w/ a known antibody attached are combined on a slide w/ a sample containing the unidentified organism various subtypes of this test can be used for specific properties (enzymes, proteins, etc.)
60
slide agglutination test: if the test antibodies recognize "epitopes" in the sample...
large aggregates of latex + antibody bound to the recognized organism will be formed
61
a positive slide agglutination test appears...
slightly translucent and foamy; expanded
62
a negative slide agglutination test appears...
mostly white and opaque
63
ELISA (enzyme-linked immunosorbent assay)
uses 2 antibodies and an enzyme substrate in a dish to identify the antigen/organism
64
ELISA: general steps?
-known "primary" antibodies attached to dish - a positive reaction results in the organism/antigen being captured by the antibody
65
ELISA: constant region definition
the Y-shaped structure where the antibodies "stick"
66
what are the 2 main types of ELISAs?
"sandwich" direct
67
what is the target in each type of ELISA?
sandwich = antigen direct = antibody
68
when an ELISA is used to determine if a patient has been exposed to and begun to respond to a pathogen, what type of ELISA is used?
antibody-capture, direct ELISA
69
when an ELISA is used to determine if a patient has an active infection of a pathogen, what type of ELISA is used?
antigen-capture, indirect/sandwich ELISA
70
when an ELISA is used to determine if a patient has been exposed to and begun to respond to a pathogen, the "bait" bound to the wells of the assay dish is...
antigen from the pathogen
71
when an ELISA is used to determine if a patient has an active infection of a pathogen, the "bait" bound to the wells of the assay dish is...
prepared (primary) antibody that recognizes the pathogen
72
when an ELISA is used to determine if a patient has an active infection of a pathogen, the secondary antibody used for detection in this type of assay must recognize and bind specifically to the...
human antibody constant region
73
when an ELISA is used to determine if a patient has an active infection of a pathogen, the secondary antibody used for detection in this type of assay must recognize and bind specifically to the...
antigen from the pathogen
74
ELISA Method A - Sandwich: step 1?
attach known "primary" antibody to the bottom of the dish
75
ELISA Method A - Sandwich: step 2?
add antigen; antigen will bind to the primary antibody
76
ELISA Method A - Sandwich: step 3?
add secondary antibody
77
ELISA Method A - Sandwich: step 4?
if the organism/antigen has bound to the primary antibody, the secondary antibody is captured
78
ELISA Method A - Sandwich: step 5?
secondary antibody covalently links to an enzyme
79
ELISA Method A - Sandwich: step 6?
substrate is added, and serves as a colorimetric indicator; goes through a color change once catalyzed by enzyme
80
ELISA Method B - direct: step 1?
attach antigen to the bottom of the dish
81
ELISA Method B - direct: step 2?
add antibodies (patient serum)
82
ELISA Method B - direct: step 3?
add secondary antibody that binds specifically to human antibodies
83
ELISA Method B - direct: step 4?
secondary antibody covalently links to an enzyme
84
ELISA Method B - direct: step 5?
add substrate; will connect to enzyme enzyme substrate is a colorimetric indicator
85
what is the difference between the sandwich and direct ELISA?
sandwich: antigen capture (entire or part of the antigen) - use antibody --> capture antigen direct: antibody capture - use antigen --> capture antibody
86
western blot
use of gel electrophoresis to transfer proteins to determine the presence of antigens
87
modern classification is heavily dependent on...
nucleic acid sequence (genome, rRNA)
88
nucleic acid hybridization
a DNA probe is hybridized to the denatured total DNA of an organism the probe is tagged with a marker that allows it to be visualized
89
in nucleic acid hybridization, how is the probe generated?
PCR (polymerase chain reaction) chemical synthesis
90
as new biotechnology develops and improves, older methods are...
being phased out and replaced by sequencing

MCB2004 (7 decks)

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