Ch. 10 - Id & Classification Of Prokaryotes

Front 1

Taxonomy

Back 1

the science that studies organisms to arrange them into groups (or taxa)

Front 2

Taxonomy shows the degree of ____________ among organisms

Back 2

similarity

Front 3

Systematics is another word for....

Back 3

phylogeny

Front 4

What is phylogeny?

Back 4

Study of the evolutionary history of organisms

(like a molecular clock)

What we are doing now - the latest.

Studying DNA & RNA of these microbes.

The more similarities they have, the closer they are to being in the same group. (And the more likely they were related to each other years and years ago.

RNA doesn't really mutate very much... (conservative) (So, if organism have similar RNA, then they haven't really changed much over millions of years that they've been here.)

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Classification involves placing organisms in groups of ___________ ___________

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related species

Front 6

Identification: matching characteristics of....

Back 6

unknown organism to known organisms

(clinical lab identification)

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The study of Phylogenetic Relationships:

1735 - Linnaeus created kingdoms of...

Back 7

Plantae & Animalia

Front 8

The study of Phylogenetic Relationships:

1800s: Bacteria & Fungi put into Kingdom _______

Kingdom _______ proposed

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Plantae

Protista

Front 9

The study of Phylogenetic Relationships:

1937 - Prokaryote introduced to distinguish _________________.

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cells without a nucleus

Front 10

The study of Phylogenetic Relationships:

1968 - Murray - introduces Kingdom _______.

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Prokaryotae

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The study of Phylogenetic Relationships:

1969 - Whittaker - introduces the ...

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5 Kindgom system

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The Three Domains:

Developed by Woese in _______

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1978

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The Three Domains:

Based on sequences of ____________ in ______________.

Back 13

nucleotides; rRNA

Front 14

What are The Three Domains:?

Back 14

1. Eukarya

2. Bacteria

3. Archaea

Front 15

Eukarya are what?

Back 15

Animals, plants, fungi, protists

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Archaea are what?

Back 16

-Methanogens

-Extreme halophiles

-Hyperthermophiles

Front 17

Phylogeny:

The 3-Domain System is based on _____________ ____________.

Back 17

evolutionary relatedness

Front 18

Phylogeny:

The 3-Domain System replaces...

Back 18

The 5-Kingdom system

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Phylogeny:

The 3-Domain System is based on obvious _____________ differences

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morphological

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Phylogeny:

The 3-Domain System does not reflect recent genetic insights of ribosomal RNA data indicating....

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that plants, animals, are more closely related than Archaea, Bacteria

Front 21

Key Concepts of the 3-Domain System:

1. All organisms evolved from...

2. The DNA passed on from ancestors is described as __________

3. The Domain Eukarya includes the Kingdoms ____________, ____________, and _____________ as well as ___________.

4. The Domains Bacteria & Archaea are ________________.

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1. cells that formed over 3 billion years ago

2. conserved (the ones that didn't mutate)

3. Fungi, Plantae, Animalia, Protists

4. Prokaryotes

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There is no Kingdom for _____________.

It goes straight from Domain to ____________.

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Prokaryotes

Phylum

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Taxonomy Hierarchy

Back 23

Look at Chart

Front 24

Classification of Eukaryotes:

Protista:

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-catch-all kingdom for a variety of organisms;

-autotrophic & heterotrophic

-grouped into "clades" based on rRNA

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Classification of Eukaryotes:

Fungi:

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-chemoheterotrophic

-unicellular or multicellular

-cell walls of chitin

-develop from spores or hyphal fragments

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Classification of Eukaryotes:

Plantae:

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-multicellular

-cellulose cell walls

-undergo photosynthesis

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Classification of Eukaryotes:

Animalia:

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-multicellular

-no cell walls

-chemoheterotrophic

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Eukaryotes originated from _______________________________

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in-foldings of of prokaryotic plasma membranes

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Endosymbiotic - what does this mean?

Back 29

That bacteria developed into organelles

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So early cells are thought to have become one of 3 things:

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1. bacteria

2. archaea

3. eukarya

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With eukaryotes, DNA inside the cell eventually formed a nucleus when...

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the cell folded in upon itself

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Bacteria formed mitochondria and chloroplasts, which are through to have...

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entered cells that contain a nucleus...

the cells fed them, and they stayed...

this is how we evolved

ENDOSYMBIOSIS:

mitochondria & chloroplasts were once free-floating bacteria. They involoped and stayed that way.

Front 33

Binomial Nomenclature means

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2 - name - naming system

(Genus, species)

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Genus is always a __________

Species is always an __________

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noun;

adjective

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Eukaryotic species is a group of morphologically similar organisms capable of ___________________________.

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producing fertile offspring

Front 36

Prokaryotic species: population of cells with

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...similar characteristics

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What is a clone?

Back 37

a population of cells with similar characteristics

(pure culture)

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What is a strain?

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A genetically different cell within a clone

Front 39

Bergen's Manual of Systematic Bacteriology:

Describes all known species and classifies according to __________ ___________.

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genetic relatedness

Front 40

Phenotypic Characteristics:

What is the important initial step?

Back 40

Microscopic morphology

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What does morphology determine?

(3 main things)

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1. size

2. shape

3. staining characteristics

Front 42

Morphology is sometimes enough to diagnose what type of eukaryotic infections?

Back 42

protozoans & fungi

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Phenotypic Characteristics:

Culture characteristics: can give clues...

1. Name a bacteria with generally small colonies

2. Which bacteria is often red at 22 d. C?

3. Which bacteria produces green pigment and has fruity odor?

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1. Streptococcus

2. Serratia marcescens

3. Pseudomonas aeruginosa

Front 44

Different media aid in identification:

1. What medium is used to ID Strep throat (Streptococcus progenies)?

2. E. coli (urinary tract infections) ferments lactose, and forms pink colonies on which media?

Back 44

1. blood agar

2. MacConkey agar

(*MacConkeys is selective AND differential - E. coli grows pink on it - Shigella is colorless on it)

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Metabolic Capabilities:

These are _______ tests and they provide more certainty of Identification.

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biochemical

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What test indicates an aerobe?

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Catalase

Front 47

Many rely on pH indicators..

looking at how they might ferment __________ or produce ___________.

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sugar;

enzymes (ex. urease)

Front 48

The basic strategy of metabolic capabilities relies on a ______________ __________.

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Dichotomous Key

Front 49

The dichotomous key is a flowchart of tests with _________ or _______ results

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positive / negative

Front 50

Give an example of a test that is accomplished without culturing?

Back 50

Breath test for ID-ing Helicobacter pylori

Front 51

Phenotypic Characteristics:

Serology: ___________________ of prokaryotic cells that can serve as identifying markers

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proteins (or polysaccharides)

Front 52

Most useful serology includes surface structures of what 4 things?

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1. cell wall

2. capsule

3. flagella

4. pili

Ex. some Streptococcus species contain unique carbohydrate in cell wall

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Serological tests use ____________ to detect...

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antibodies

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True or False:

Antibodies are specific.

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TRUE

Front 55

Fatty Acid Analysis

(FAME = fatty acid methyl ester)

Uses fatty acid ___________

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ratios

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Fatty Acid Analysis

Prokaryotic species differ in TYPE and QUANTITY of fatty acids in ____________.

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membranes

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Fatty Acid Analysis

Organisms are treated to _________________.

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release fatty acids

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Fatty Acid Analysis

Fatty acids converted to:

Back 58

FAME (fatty acid methyl ester) form

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Fatty Acid Analysis

FAMEs are separated and measured via what VERY SPECIFIC equipment?

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gas chromatography

(produces a "chart" of spikes)

*The resulting chromatogram is compared to known species

Front 60

Genotypic Characteristics:

Detecting Specific nucleotide sequences...

Nucleic acid probes locate nucleotide sequence characteristic of species or group by ___________________

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binding a tagged compliment to that species

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How does that work?

1. DA strands are labelled and __________.

2. These labeled / tagged (marked) probes are added to bind to...

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1. separated by heating (denaturing)

2. the compliment

**if a probe binds to DNA, then known organisms can be Identified.

Front 62

Detecting Specific Nucleotide Sequences:

Nucleic Acid Amplification Test (NAAT) is used to _____________

(being used more and more in forensics)

Back 62

increase # of copies of specific DNA sequences

(like creating back ups or photocopies so that we can go back and put in probes)

(some organisms are hard to culture - don't know what they are / what they like)

Front 63

the NAAT tests allow for detection of ____________ numbers of organisms, often from...

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small numbers;

soil, body fluids, food, water

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NAAT test are useful for detecting organisms that cannot be ___________.

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cultured

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Polymerase chain reaction () is another common technique

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PCR - also make copies

- process works like a copy machine through using temperature to separate DNA strands, add DNA polymerase which binds to strands, then separate them again

--all base on splitting apart, reading it, make a photocopy

*PCRs can more than double the amount of DNA that you have in an hour

*used a lot when we don't have enough of the DNA

Front 66

Genotypical Characteristics

Sequencing Ribosomal RNA Genes:

uses one of which two things?

****RNA NEVER MUTATES

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1. ribosomal RNA

or

2. encoding DNA (rDNA)

****RNA NEVER MUTATES (really conservative)

Front 67

Genotypical Characteristics

Sequencing Ribosomal RNA Genes:

Which is the most useful rRNA because of its moderate size?

How many nucleotides does it have?

Back 67

16 S rRNA

1500 (that's small!)

*really like to use it because it does not mutate (is conservative)

*we will read the 16 S rRNA for as many microbes as we've got that match it in our database, and see if it matches anything in database - do it to unknown and match to database

Front 68

Genotypical Characteristics

Sequencing Ribosomal RNA Genes:

Sequence is compared with ___________

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extensive databases

(like taking a fingerprint and running it in the system)

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Genotypical Characteristics

Sequencing Ribosomal RNA Genes:

Why is this a useful test (2 reasons)

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1. can identify organisms in small numbers

2. cani identify organisms that cannot be grown in cultures

Front 70

Characterizing Strain Differences:

Terminology:

A strain is a subset of bacterial species that ....

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differ from other bacteria of the same species by some minor but identifiable difference

Front 71

Characterizing Strain Differences:

A strain is a population of organisms that descends from....

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a single organism or pure culture isolate.

Stains within a species may differ slightly from one another in many ways

Front 72

Characterizing Strain Differences:

Example: Certain types (or strains) of E. coli can cause food poisoning, but one particular strain ___________ can cause a severe case of food poisoning.

Back 72

E. coli O157:H7

(The H is on the flagella)

Front 73

Characterizing Strain Differences:

Biochemical Typing

This is a group with characteristic biochemical patterns called either a ____ or ______.

Back 73

biovar; biotype

(more of a biochemical pattern than serovar - another way of typing strains)

Front 74

Characterizing Strain Differences:

Serological Typing:

E. coli distinguished by _____________ type of flagella, capsules, lipopolysaccharides...

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antigenic

Front 75

Serological typing is group with characteristic ANTIGENS, called either a _______ or a _______.

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Serovar; serotype

SEROVAR = a certain typing of a strain

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Characterizing Strain Differences:

Name 3 Methods

Back 76

1. Molecular Typing

2. Phage Typing

3. Antibiograms

Front 77

Characterizing Strain Differences:

Molecular Typing: 4 steps

(molecular typing = electrophoresis = DNA FINGERPRINT)

Back 77

1. Cut DNA samples w/same restriction enzyme

2. Separate via gel electrophoresis

3. Patterns called RFLPs (restriction fragment length polymorphisms

4. Different RFLPs indicate different strains

******

Restrictive enzymes look for a particular pattern on the DNA and cuts it there.

We put these restrictive enzymes into the DNA to do the cutting for us.

Looks for the specific pattern, ex. GATTAC - it will cut on one side of that pattern wherever it appears, which creates pieces of different lengths.

Next, those different lengths / pieces get put into a gel (like a sponge) with big & little holes.

Current runs through the gel.

The pieces have a NEG charge and will want to go toward the positive charge. The shorter pieces will get there first (faster). You time it, pull the current away at a specific time, and this leaves you with a pattern.

You can freeze the frame to give you an image of this pattern and can compare this pattern to a known pattern in the CDC database.

Ex. - this is how we make insulin (by inserting the human gene that makes insulin into a bacterial / yeast cell - it will start making insulin.)

Front 78

Characterizing Strain Differences:

What is the name of the CDC database that tracks food borne pathogens?

Back 78

Pulse Net

Front 79

Characterizing Strain Differences:

What is the newest method of molecular typing called?

Back 79

Multilocus sequence typing (MLST)

Front 80

Characterizing Strain Differences:

Phage Typing relies on __________________.

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Differences in susceptibility to bacteriophages

(viruses that attack bacteria) - very specific

*Susceptibility pattern can be determined with bacteria & different bacteriophage suspensions

*uses disc diffusion / zone of inhibitions

Front 81

Characterizing Strain Differences:

Which is more commonly used:

Phage typing or Molecular Typing

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Molecular typing has largely replaced phage typing

Front 82

Characterizing Strain Differences:

Phage typing is still useful in labs that lack...

Back 82

genomic testing equipment

Front 83

Characterizing Strain Differences:

Antibiograms - test for _________________.

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antibiotic susceptibility patterns

(clearing zone around antibiotic discs)

Ex. Pseudomonas - resistant to everything

(antibiograms largely replaced by molecular typing)

Front 84

Classifying Prokaryotes:

Classification has historically been base on ____________ traits such as... (list 4)

Back 84

Phenotypic:

-size

-shape

-staining

-metabolic capabilities

Front 85

Why is classifying prokaryotes by phenotypic traits not the best method?

Back 85

Phenotypically similar organisms may be only distantly related.

Conversely, closely related organisms may appear dissimilar.

Ex. - we are more closely related to slime molds

Front 86

Classifying Prokaryotes:

Which techniques are the most accurate?

Back 86

Molecular typing

Front 87

Classifying Prokaryotes:

DNA sequences are viewed as __________ ______________.

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evolutionary chronometers (molecular clock)

(Provide a relative measure of time elapsed since divergence from common ancestor)

*We use these to start to predict what flus are coming around next - can see which viruses mutate more than others, etc.

Front 88

Classifying Prokaryotes:

The more time elapsed since divergence from the common ancestor, the _____________ the DNA sequence differences.

Back 88

GREATER

Front 89

Classifying Prokaryotes:

DNA sequencing allows the construction of a ___________ ____________.

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Phylogenic Tree

Front 90

Classifying Prokaryotes:

The less time that has elapsed since divergence from common ancestor....

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the more closely you are related

Front 91

Classifying Prokaryotes:

The Phylogenic Tree shows....

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evolutionary relatedness

(But DNA sequencing also highlights obstacle)

Front 92

Name something that complicates DNA comparisons. Why?

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Horizontal gene transfer

*DNA is transferred to another species

*Ex. bacterium Thermatogo maritima appear to have acquired 25% of their genes from archaealspecies.

Front 93

Classifying Prokaryotes:

Instead of a tree, some scientists propose...

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a shrub with interwoven branches

Front 94

Classifying Prokaryotes:

GENOTYPIC Characteristics

Name 4 Methods:

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1. 16S rDNA Sequence Analysis (genes that code for the rRNA)

2. DNA hybridization

3. DNA Base Ratio (C & G content)

4. Phenotypic Methods

Front 95

Classifying Prokaryotes:

Which is more accurate: Genotypic or Phenotypic characteristics?

Back 95

Genotypic

(Differences in DNA sequences can be used to determine the point in time at which two organisms diverged from a common ancestor)

Front 96

Classifying Prokaryotes:

Why are phenotypic characteristics not as reliable?

Back 96

Properties such as ability to degrade lactose and the presence of flagella do not necessarily reflect the evolutionary relatedness of organisms.

Front 97

Classifying Prokaryotes:

16S rRNA Sequence Analysis

Back 97

Comparisons revolutionized classification

Sequences highly conserved since function critical

Front 98

Classifying Prokaryotes:

16S rRNA Sequence Analysis:

_______________ of ________________ allow for identification of distant relatedness

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lack of mutations

No horizontal gene transfer

stable, conservative

Front 99

Classifying Prokaryotes:

16S rRNA Sequence Analysis:

Certain regions relatively reliable; can determine recent _____________

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divergence

Front 100

Classifying Prokaryotes:

16S rRNA Sequence Analysis:

What type of gene transfer appears rare?

Back 100

Horizontal

Front 101

Classifying Prokaryotes:

16S rRNA Sequence Analysis:

Culturing...

Back 101

is not necessary...

can take organism straight from the environment

Front 102

Classifying Prokaryotes:

16S rRNA Sequence Analysis:

May not resolve at species level since...

Back 102

closely related prokaryotes can have identical 16S rRNA sequences

(in theses cases, DNA hybridization is a better tool)

Front 103

Classifying Prokaryotes:

DNA Hybridization

Relatedness of organisms can be determined by...

Back 103

similarity of nucleotide sequences

(sequence homology measured by DNA hybridization)

*unzip it, compare it

Front 104

Classifying Prokaryotes:

DNA Hybridization -

Extent of hybridization reflects...

Back 104

degree of similarity

Front 105

Classifying Prokaryotes:

DNA Hybridization

Uses...

Back 105

complimentary base pairing of single strands

(If there is a high percentage of pairings that happen, organism is considered related)

70% similarity = same species

Front 106

Classifying Prokaryotes:

DNA Hybridization:

Based on DNA Hybridization, which two bacteria ought to be related?

Back 106

Shigella & E. coli

Front 107

Classifying Prokaryotes:

DNA Base Ratio (C & G Content)

Looks at the ratio of bases in DNA:

Back 107

(A:T and G:C)

Front 108

Classifying Prokaryotes:

DNA Base Ratio -

Base Ratio is expressed as either:

Back 108

1. G + C content

or

2. GC content

Front 109

Classifying Prokaryotes:

DNA Base Ratio -

If ratio deviates by more than a few percent...

Back 109

organisms are not related

(counting how many Gs and Cs there are)

(and from there can figure out how many As and Ts)

Front 110

Classifying Prokaryotes:

DNA Base Ratio -

Similarity does NOT mean relatedness because...

Back 110

the nucleotide sequences could differ

Front 111

Dichotomous Key for Classifying / Identifying Microorganisms:

What are the 3 main categories it branches into?

Back 111

1. Phenotypic characteristics

2. Genotypic characteristics

3. Strain Differences

Front 112

look at last slide of Ch. 10 power point

Back 112

for branches underneath these...

Front 113

Extra -

Back 113

Salmonella produces gas and black color

Front 114

Phenotypical Characteristics

Name 3 type of tests / techniques:

Back 114

Metabolic

Morphology

Serology

Front 115

Genotypical Characteristics:

Anything with __________ or ________

Back 115

DNA or RNA

Front 116

With Genotype Tests we are either...

Back 116

1. making copies of the DNA to work with

2. split it apart (using nucleic acid probes, which is a compliment - a certain pattern for a certain known organism...see if they hook up to each other.