Chap 10 Flashcards
(148 cards)
1
Q
Taxonomy
A
the science of classifying organisms
2
Q
Taxonomy shows
A
degree of similarity among organisms
3
Q
Systematics, or phylogeny
A
the study of the evolutionary history of organisms
4
Q
1735: Linnaeus contribution
A
kingdoms Plantae and Animalia
5
Q
1800s: Bacteria and fungi put in
A
kingdom Plantae (Nägeli)
6
Q
1800s Kingdom Protista proposed for
A
bacteria, protozoa, algae, and fungi (Haeckel)
7
Q
1937: Prokaryote introduced to
A
distinguish cells without a nucleus
8
Q
1968: Murray
A
kingdom Prokaryotae
9
Q
1969: Whittaker
A
five-kingdom system
10
Q
Of what value is taxonomy and systematics?
A
provide a standardized way to identify, name, and classify organisms, allowing scientists to effectively communicate about species, understand their evolutionary relationships, and study biodiversity,
11
Q
Why shouldn’t bacteria be placed in the plant kingdom?
A
Because bacteria are prokaryotic, they do not have a nucleus and no membrane-bound organelles.
12
Q
Who developed the three domains?
A
Woese in 1978
13
Q
What are the three domains based on?
A
based on sequences of nucleotides in rRNA
14
Q
What are the three domains?
A
Eukarya
Bacteria
Archaea
15
Q
Eukarya
A
Animals, plants, fungi, protists
16
Q
Archaea
A
Methanogens
Extreme halophiles
Hyperthermophiles
17
Q
Key concepts of three domain system
A
- All organisms evolved from cells that formed over 3 billion years ago.
- The DNA passed on from ancestors is described as conserved.
- Domain Eukarya includes the kingdoms Fungi, Plantae, and Animalia, as well as protists. The Domains Bacteria and Archaea are prokaryotes.
18
Q
Cell wall of Archaea contains
A
Varies in composition; no peptidoglycan
19
Q
Cell wall of bacteria contains
A
peptidoglycan
20
Q
Cell wall of eukarya
A
Varies in composition; contains carbohydrates
21
Q
Fist amino acid in protein synthesis of archaea
A
methionine
22
Q
Fist amino acid in protein synthesis of bacteria
A
formylmethionine
23
Q
Fist amino acid in protein synthesis of eukarya
A
methionine
24
Q
antibiotic sensitivity of archaea
A
no
25
antibiotic sensitivity of bacteria
yes
26
antibiotic sensitivity of eukarya
no
27
rRNA loop
binds to ribosomal protein, found in all bacteria
28
Does archaea have an rRNA loop?
no
29
Does bacteria have an rRNA loop?
yes
30
Does Eukarya have an rRNA loop?
no
31
DNA of prokaryotes
one circular; some two circular; some linear
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DNA of eukaryotic cell
linear
33
Eukaryotic organelles DNA
circular
34
Histones are found in
prokaryotic cell archaea and eukaryotic cells
35
Types of ribosomes in prokaryotic cells?
70 S
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Types of ribosomes in eukaryotic cells
80 S
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How do prokaryotic cells grow?
Binary fission
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How do eukaryotic cells grow?
Mitosis
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How do eukaryotic organelles (mitochondria and chloroplasts grow?)
binary fission
40
Eukaryotes originated from
infoldings of prokaryotic plasma membranes
Endosymbiotic bacteria developed into organelles
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What does a phylogenetic tree do?
Groups organisms according to common properties
42
A phylogenetic tree Groups organisms according to common properties such as
Fossils
-Genomes
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Mutations accumulated in the genomes serve as
molecular clock
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concepts behind phylogenetic tree
1. Groups of organisms evolved from a common ancestor
2. Each species retains some characteristics of its ancestor
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stromatolites
rock-like pillars. Layered sedimentary formations that are some of the oldest fossils on Earth.
46
What evidence supports classifying organisms into three domains?
1. differences in the sequences of nucleotides in the cell's ribosomal RNAs (rRNA),
2. the cell's membrane lipid structure
3. its sensitivity to antibiotics
47
Compare archaea and bacteria; bacteria and eukarya; and archaea and eukarya.
Both Bacteria and Archaea are prokaryotes, single-celled microorganisms with no nuclei, and Eukarya includes us humans and all other animals, plants, fungi, and single-celled protists; all Eukarya are organisms whose cells have nuclei to enclose their DNA apart from the rest of the cell.
48
Why do we need scientific nomencature?
Common names vary with languages and geography
49
Binomial nomenclature
is used worldwide to consistently and accurately name organisms
50
Parts of binomial nomenclature
1. Genus
2. Specific epithet (species)
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entero-
intestines
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pyo-
pus
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cerevisia
beer
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chryso-
yellow pigment
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-myces
fungus
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penicill
tuft-like or paintbrush
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trypano-, borer
corkscrew
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soma
body
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What is the The Taxonomic Hierarchy
subdivisions developed by Linnaeus to classify plants and animals
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Taxonomic hierarchy was developed by
Linnaeus
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Eukaryotic species:
a group of closely related organisms that breed among themselves
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Taxonomic hierarchy parts
D- Kings play chess on fancy glass stools
1. All organisms
2. Domain
3. Kingdom
4. Phylum
5. Class
6. Order
7. Family
8. Genus
9. Species
63
Using Escherichia coli and Entamoeba coli as examples, explain why the genus name must always be written out on first use. Why is binomial nomenclature preferable to common names?
To avoid confusing organism that have a genus that starts with the same letter. Binomial nomenclature provides standardization
64
Find the gram-positive bacteria Staphylococcus in Appendix F. To which bacteria is this genus more closely related: Bacillus or Streptococcus?
Bacillus because they're in the same order
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genus consists of
species that differ from each other in certain ways but are related by descent.
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family
related genera
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Prokaryotic species
population of cells with similar characteristics
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Culture
bacteria grown in laboratory media
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Clone
population of cells derived from a single parent cell
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Strain:
genetically different cells within a clone
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Protista:
catchall kingdom for a variety of organisms; autotrophic and heterotrophic
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Protista are grouped into
Clades
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Clades are based on
rRNA
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Fungi can be
chemoheterotrophic; unicellular or multicellular;
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Fungi cell walls
chitin
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Fungi develop from
spores or hyphal fragments
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Plantae:
multicellular; cellulose cell walls; undergo photosynthesis
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Animalia:
multicellular; no cell walls; chemoheterotrophic
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multicellular; no cell walls; chemoheterotrophic
Animalia
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Viruses are not a part of
any domain
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Viral species
population of viruses with similar characteristics that occupies a particular ecological niche
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Use the terms species, culture, clone, and strain in one sentence to describe growing methicillin-resistant Staphylococcus aureus (MRSA).
A laboratory might cultivate a specific "strain" of the bacterial "species" Staphylococcus aureus, which is resistant to methicillin, by growing a "clone" from a particular "culture" of MRS
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You discover a new multicellular, nucleated, heterotrophic, organism with cell walls. To what kingdom does it belong?
fungi
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protist
unicellular eukaryotes and their close relatives.
85
Why doesn't the definition of a viral species work for a bacteria?
viruses are not made from cells
86
Classification
placing organisms in groups of related species
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Identification
matching characteristics of an "unknown" organism to lists of known organisms
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Bergey's Manual of Determinative Bacteriology
provides identification schemes for identifying bacteria and archaea
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Approved Lists of Bacterial Names
lists species of known classification
90
In clinical microbiology, lab requisition forms are used to
note types of specimens collected and tests to be conducted
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Transport media
is used to collect and transport pathogens to a laboratory
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Morphological characteristics useful for
for identifying eukaryotes; tell little about phylogenetic relationships
93
Differential staining:
Gram staining, acid-fast staining; not useful for bacteria without cell walls
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Biochemical tests:
determine presence of bacterial enzymes
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Rapid identification methods
1. perform several biochemical tests simultaneously
2. Results of each test are assigned a number
96
Automated rapid identification system is available for
medically important bacteria and yeast
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The data from a mass spectrophotometer are compared to
a database
98
serology
The science that studies serum and immune responses in serum
99
Microorganisms are antigenic
they stimulate the body to form antibodies in the serum
100
In an antiserum,
solution of antibodies is tested against an unknown bacterium
101
slide agglutination test
bacteria agglutinate when mixed with antibodies produced in response to the bacteria
102
Serological testing can differentiate between
species and strains within species
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Enzyme-linked immunosorbent assay (ELISA)
Known antibodies and an unknown type of bacterium are added to a well; a reaction identifies the bacteria
104
Western blotting
Identifies antibodies in a patient's serum; confirms HIV infection, and Lyme disease
105
How does the ELISA method work?
1. Antibody is adsorbed to well
2. Patient sample is added; complimentary antigen binds to antibody
3. Enzyme-linked antibody specific for test antigen is added and bindsto antigen, forming a sandwich
4. Enzyme's substrate is added, and reaction produces a product that causes a visible color change
106
Phage typing
Test for determining which phages a bacterium is susceptible to. A method of identifying bacteria using specific strains of bacteriophages
107
How does phage typing occur?
On a plate, clearings called plaques appear where phages infect and lyse bacterial cells
108
FAMEs: Fatty acid methyl esters
provide profiles that are constant for a particular species
109
Flow cytometry uses
Uses differences in electrical conductivity between species or fluorescence
110
What is flow cytometry?
A method of counting cells using a flow cytometer, which detects cells by the presence of a fluorescent tag on the cell surface.
111
function of DNA sequencing for identification?
Taxonomists can use an organism’s DNA base composition to draw conclusions about relatedness.
112
This base composition is usually expressed as
percentage of guanine plus cytosine (G + C).
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Two organisms that are closely related have similar amounts of
various bases
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Why can you use base composition to find relatedness?
base composition of a single species is theoretically a fixed property
115
However, if there is a difference of more than 10% in their percentage of GC pairs
ex: One bacterium’s DNA contains 40% GC and another bacterium has 60% GC
these two organisms probably aren’t related.
116
Genetic sequences of hundreds of organisms are compiled in databases that can be used online through the
NCBI
117
DNA fingerprinting
Analysis of DNA by electrophoresis of restriction enzyme fragments of DNA
118
Why does DNA fingerprinting work?
Comparing the number and sizes of restriction fragments that are produced from different organisms provides information about their genetic similarities and differences;
119
the more similar the patterns, or DNA fingerprints,
the more closely related the organisms are expected to be
120
DNA fingerprinting is used to determine the source of
hospital acquired infections
121
Nucleic acid hybridization measures
the ability of DNA strands from one organism to hybridize with DNA strands of another organism
122
Greater degree of hybridization means
greater degree of relatedness
123
Hybridization of >70% indicates
same species
124
Steps of DNA hybridization
1. Heat to separate strands
2. Combine single strands of DNA
3. Cool to allow renaturation of double stranded DNA
4. Determine degree of hybridization
125
complete hybridization
organisms identical
126
Partial hybridization
organisms related
127
No hybridization
organisms unrelated
128
Nucleic Acid Amplification Tests (NAATs)
use PCR to amplify DNA of an unknown microorganism that cannot be cultured
129
PCR
A technique using DNA polymerase to make multiple copies of a DNA template in vitro.
130
Southern blotting
uses nucleic acid hybridization to identify unknown microorganisms using DNA probes
131
DNA probes
A short, labeled, single strand of DNA or RNA used to locate its complementary strand in a quantity of DNA.
132
A DNA chip (also known as a microarray) contains
DNA probes and detects pathogens by hybridization between the probe and DNA in the sample
133
DNA chip is detected by
fluorescence
134
a DNA CHIP CAN BE MANUFACTURED TO CONTAIN
Hundreds of housands of synthetic, single stranded DNA sequences. Assume that each DNA sequence was unique to a different gene
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A silica wafer that holds DNA probes; used to recognize DNA in samples being tested.
DNA chip
136
Ribotyping
rRNA sequencing
137
Fluorescent in situ hybridization (FISH)
Fluorescent DNA or RNA probes stain the microorganisms being targeted
138
Fluorescent in situ hybridization (FISH) determines
Determines the identity, abundance, and relative activity of microorganisms in an environment
139
Dichotomous keys
Identification keys based on successive questions
140
Cladograms
Maps that show evolutionary relationships among organisms; based on rRNA sequences
141
Main method to identify bacteria
Chemical tests
142
Dichotomous keys
series of paired statements in which one of each pair of statements applies to a given organism. Provide step by step procedure for identifying an organism.
143
What is in Bergey's Manual?
the standard laboratory identification reference on bacteria.
144
What is tested in Western blotting and Southern blotting?
Southern blot detects specific DNA sequences, Northern blot detects particular RNA sequences, and Western blot detects specific proteins
145
What is identified by phage typing?
method for identifying bacterial strains by infecting them with bacteriophages, or phages, and observing the bacteria's response
146
Why does PCR identify a microbe?
it can amplify a specific segment of DNA, which allows for the detection and identification of gene sequences
147
Which techniques involve nucleic acid hybridization?
Southern blotting, Northern blotting, in situ hybridization (ISH), fluorescence in situ hybridization (FISH), polymerase chain reaction (PCR), and DNA microarrays
148
Is a cladogram used for identification or classification?
used in classification to visually represent similarities between organisms
