Chap 10 Flashcards
Taxonomy
the science of classifying organisms
Taxonomy shows
degree of similarity among organisms
Systematics, or phylogeny
the study of the evolutionary history of organisms
1735: Linnaeus contribution
kingdoms Plantae and Animalia
1800s: Bacteria and fungi put in
kingdom Plantae (Nägeli)
1800s Kingdom Protista proposed for
bacteria, protozoa, algae, and fungi (Haeckel)
1937: Prokaryote introduced to
distinguish cells without a nucleus
1968: Murray
kingdom Prokaryotae
1969: Whittaker
five-kingdom system
Of what value is taxonomy and systematics?
provide a standardized way to identify, name, and classify organisms, allowing scientists to effectively communicate about species, understand their evolutionary relationships, and study biodiversity,
Why shouldn’t bacteria be placed in the plant kingdom?
Because bacteria are prokaryotic, they do not have a nucleus and no membrane-bound organelles.
Who developed the three domains?
Woese in 1978
What are the three domains based on?
based on sequences of nucleotides in rRNA
What are the three domains?
Eukarya
Bacteria
Archaea
Eukarya
Animals, plants, fungi, protists
Archaea
Methanogens
Extreme halophiles
Hyperthermophiles
Key concepts of three domain system
- 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.
Cell wall of Archaea contains
Varies in composition; no peptidoglycan
Cell wall of bacteria contains
peptidoglycan
Cell wall of eukarya
Varies in composition; contains carbohydrates
Fist amino acid in protein synthesis of archaea
methionine
Fist amino acid in protein synthesis of bacteria
formylmethionine
Fist amino acid in protein synthesis of eukarya
methionine
antibiotic sensitivity of archaea
no
antibiotic sensitivity of bacteria
yes
antibiotic sensitivity of eukarya
no
rRNA loop
binds to ribosomal protein, found in all bacteria
Does archaea have an rRNA loop?
no
Does bacteria have an rRNA loop?
yes
Does Eukarya have an rRNA loop?
no
DNA of prokaryotes
one circular; some two circular; some linear
DNA of eukaryotic cell
linear
Eukaryotic organelles DNA
circular
Histones are found in
prokaryotic cell archaea and eukaryotic cells
Types of ribosomes in prokaryotic cells?
70 S
Types of ribosomes in eukaryotic cells
80 S
How do prokaryotic cells grow?
Binary fission
How do eukaryotic cells grow?
Mitosis
How do eukaryotic organelles (mitochondria and chloroplasts grow?)
binary fission
Eukaryotes originated from
infoldings of prokaryotic plasma membranes
Endosymbiotic bacteria developed into organelles
What does a phylogenetic tree do?
Groups organisms according to common properties
A phylogenetic tree Groups organisms according to common properties such as
Fossils
-Genomes
Mutations accumulated in the genomes serve as
molecular clock
concepts behind phylogenetic tree
- Groups of organisms evolved from a common ancestor
- Each species retains some characteristics of its ancestor
stromatolites
rock-like pillars. Layered sedimentary formations that are some of the oldest fossils on Earth.
What evidence supports classifying organisms into three domains?
- differences in the sequences of nucleotides in the cell’s ribosomal RNAs (rRNA),
- the cell’s membrane lipid structure
- its sensitivity to antibiotics
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.
Why do we need scientific nomencature?
Common names vary with languages and geography
Binomial nomenclature
is used worldwide to consistently and accurately name organisms
Parts of binomial nomenclature
- Genus
- Specific epithet (species)
entero-
intestines
pyo-
pus
cerevisia
beer
chryso-
yellow pigment
-myces
fungus
penicill
tuft-like or paintbrush
trypano-, borer
corkscrew
soma
body
What is the The Taxonomic Hierarchy
subdivisions developed by Linnaeus to classify plants and animals
Taxonomic hierarchy was developed by
Linnaeus
Eukaryotic species:
a group of closely related organisms that breed among themselves
Taxonomic hierarchy parts
D- Kings play chess on fancy glass stools
- All organisms
- Domain
- Kingdom
- Phylum
- Class
- Order
- Family
- Genus
- Species
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
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
genus consists of
species that differ from each other in certain ways but are related by descent.
family
related genera
Prokaryotic species
population of cells with similar characteristics
Culture
bacteria grown in laboratory media
Clone
population of cells derived from a single parent cell
Strain:
genetically different cells within a clone
Protista:
catchall kingdom for a variety of organisms; autotrophic and heterotrophic
Protista are grouped into
Clades
Clades are based on
rRNA
Fungi can be
chemoheterotrophic; unicellular or multicellular;
Fungi cell walls
chitin
Fungi develop from
spores or hyphal fragments
Plantae:
multicellular; cellulose cell walls; undergo photosynthesis
Animalia:
multicellular; no cell walls; chemoheterotrophic
multicellular; no cell walls; chemoheterotrophic
Animalia
Viruses are not a part of
any domain
Viral species
population of viruses with similar characteristics that occupies a particular ecological niche
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
You discover a new multicellular, nucleated, heterotrophic, organism with cell walls. To what kingdom does it belong?
fungi
protist
unicellular eukaryotes and their close relatives.
Why doesn’t the definition of a viral species work for a bacteria?
viruses are not made from cells
Classification
placing organisms in groups of related species
Identification
matching characteristics of an “unknown” organism to lists of known organisms
Bergey’s Manual of Determinative Bacteriology
provides identification schemes for identifying bacteria and archaea
Approved Lists of Bacterial Names
lists species of known classification
In clinical microbiology, lab requisition forms are used to
note types of specimens collected and tests to be conducted
Transport media
is used to collect and transport pathogens to a laboratory
Morphological characteristics useful for
for identifying eukaryotes; tell little about phylogenetic relationships
Differential staining:
Gram staining, acid-fast staining; not useful for bacteria without cell walls
Biochemical tests:
determine presence of bacterial enzymes
Rapid identification methods
- perform several biochemical tests simultaneously
- Results of each test are assigned a number
Automated rapid identification system is available for
medically important bacteria and yeast
The data from a mass spectrophotometer are compared to
a database
serology
The science that studies serum and immune responses in serum
Microorganisms are antigenic
they stimulate the body to form antibodies in the serum
In an antiserum,
solution of antibodies is tested against an unknown bacterium
slide agglutination test
bacteria agglutinate when mixed with antibodies produced in response to the bacteria
Serological testing can differentiate between
species and strains within species
Enzyme-linked immunosorbent assay (ELISA)
Known antibodies and an unknown type of bacterium are added to a well; a reaction identifies the bacteria
Western blotting
Identifies antibodies in a patient’s serum; confirms HIV infection, and Lyme disease
How does the ELISA method work?
- Antibody is adsorbed to well
- Patient sample is added; complimentary antigen binds to antibody
- Enzyme-linked antibody specific for test antigen is added and bindsto antigen, forming a sandwich
- Enzyme’s substrate is added, and reaction produces a product that causes a visible color change
Phage typing
Test for determining which phages a bacterium is susceptible to. A method of identifying bacteria using specific strains of bacteriophages
How does phage typing occur?
On a plate, clearings called plaques appear where phages infect and lyse bacterial cells
FAMEs: Fatty acid methyl esters
provide profiles that are constant for a particular species
Flow cytometry uses
Uses differences in electrical conductivity between species or fluorescence
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.
function of DNA sequencing for identification?
Taxonomists can use an organism’s DNA base composition to draw conclusions about relatedness.
This base composition is usually expressed as
percentage of guanine plus cytosine (G + C).
Two organisms that are closely related have similar amounts of
various bases
Why can you use base composition to find relatedness?
base composition of a single species is theoretically a fixed property
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.
Genetic sequences of hundreds of organisms are compiled in databases that can be used online through the
NCBI
DNA fingerprinting
Analysis of DNA by electrophoresis of restriction enzyme fragments of DNA
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;
the more similar the patterns, or DNA fingerprints,
the more closely related the organisms are expected to be
DNA fingerprinting is used to determine the source of
hospital acquired infections
Nucleic acid hybridization measures
the ability of DNA strands from one organism to hybridize with DNA strands of another organism
Greater degree of hybridization means
greater degree of relatedness
Hybridization of >70% indicates
same species
Steps of DNA hybridization
- Heat to separate strands
- Combine single strands of DNA
- Cool to allow renaturation of double stranded DNA
- Determine degree of hybridization
complete hybridization
organisms identical
Partial hybridization
organisms related
No hybridization
organisms unrelated
Nucleic Acid Amplification Tests (NAATs)
use PCR to amplify DNA of an unknown microorganism that cannot be cultured
PCR
A technique using DNA polymerase to make multiple copies of a DNA template in vitro.
Southern blotting
uses nucleic acid hybridization to identify unknown microorganisms using DNA probes
DNA probes
A short, labeled, single strand of DNA or RNA used to locate its complementary strand in a quantity of DNA.
A DNA chip (also known as a microarray) contains
DNA probes and detects pathogens by hybridization between the probe and DNA in the sample
DNA chip is detected by
fluorescence
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
A silica wafer that holds DNA probes; used to recognize DNA in samples being tested.
DNA chip
Ribotyping
rRNA sequencing
Fluorescent in situ hybridization (FISH)
Fluorescent DNA or RNA probes stain the microorganisms being targeted
Fluorescent in situ hybridization (FISH) determines
Determines the identity, abundance, and relative activity of microorganisms in an environment
Dichotomous keys
Identification keys based on successive questions
Cladograms
Maps that show evolutionary relationships among organisms; based on rRNA sequences
Main method to identify bacteria
Chemical tests
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.
What is in Bergey’s Manual?
the standard laboratory identification reference on bacteria.
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
What is identified by phage typing?
method for identifying bacterial strains by infecting them with bacteriophages, or phages, and observing the bacteria’s response
Why does PCR identify a microbe?
it can amplify a specific segment of DNA, which allows for the detection and identification of gene sequences
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
Is a cladogram used for identification or classification?
used in classification to visually represent similarities between organisms
