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MICROBIO BIOL-160 LEC > Classifying and Identifying Microorganisms > Flashcards

Classifying and Identifying Microorganisms Flashcards

1
Q

definition of TAXONOMY

A

TAXONOMY:
the science of classification of LIVING FORMS

  • helps with establishing relationships and differences between GROUP OF ORGANISMS
  • common reference for IDENTIFYING ORGANISMS
  • a UNIVERSAL LANGUAGE
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2
Q

how does MODERN TAXONOMY differ now?

A
  • much more DYNAMIC–now have the ability to RAPIDLY SEQUENCE ENTIRE GENOMES and get new INSIGHT into classification and evolution
  • before: used to SEQUENCE BY HAND
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3
Q

describe TWO KINGDOM CLASSIFICATION

A

classified by CARL LINNAEUS in 1735
- classified under PLANTS and ANIMALS

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4
Q

what is the current system for DOMAINS?

A

CURRENT–THREE-DOMAIN-SYSTEM:
- BACTERIA (have prokaryotic cells)
- ARCHAEA (have prokaryotic cells)
- EUKARYA (have eukaryotic cells)

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5
Q

what was the TRADITIONAL FIVE-KINGDOM SYSTEM?

A
  • MONERA
  • PROTISTA
  • PLANTAE
  • FUNGI
  • ANIMALIA
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6
Q

what was the SIX-KINGDOM SYSTEM?

A
  • BACTERIA
  • ARCHAEA
    (part of the original “MONERA” system)
  • PROTISTA
  • PLANTAE
  • FUNGI
  • ANIMALIA
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7
Q

definition of domain

A

the BROADEST TAXONOMIC GROUP

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8
Q

definition of MODERN TAXONOMY

A

MODERN TAXONOMT:
- reflects the PHYLOGENETIC RELATIONSHIP of organisms
- shows the EVOLUTIONARY RELATIONSHIP among various species

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9
Q

definition of PHYLOGENY

A

PHYLOGENY:
- the HISTORY of the EVOLUTION of a species or a group of organisms
- based on EVOLUTIONARY DEVELOPMENT

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10
Q

what is a PHYLOGENETIC TREE?

A

a specific DIAGRAMMATIC GROUPING of organisms according to COMMON EVOLUTIONARY HISTORY
- indication of COMMON TRAITS that implies that a GROUP OF ORGANISMS evolved from COMMON ANCESTOR
- all branches from a COMMON ANCESTOR to PRESENT-DAY SPECIES

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11
Q

describe some CHARACTERISTICS of ARCHAEA

A

CELL TYPE:
- prokaryotic

CELL WALL:
- can vary; has NO PEPTIDOGLYCAN

MEMBRANE LIPIDS:
- composed of BRANCHED CARBON CHAINS–attached to GLYCEROL

FIRST AMINO ACID:
- METHIONINE (MET)

ANTIBIOTIC SENSITIVITY:
- X

rRNA LOOP:
- lacking

COMMON ARM of tRNA:
- lacking

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12
Q

describe some CHARACTERISTICS of BACTERIA

A

CELL TYPE:
- prokaryotic

CELL WALL:
- has PEPTIDOGLYCAN

MEMBRANE LIPIDS:
- has STRAIGHT CARBON CHAINS–attached to GLYCEROL, ESTER LINKAGE

FIRST AMINO ACID:
- METHIONINE (MET)

ANTIBIOTIC SENSITIVITY:
- YES

rRNA LOOP:
- YES

COMMON ARM of tRNA:
- YES

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13
Q

describe some CHARACTERISTICS of EUKARYA

A

CELL TYPE:
- eukaryotic

CELL WALL:
- can vary; contains CARBS

MEMBRANE LIPIDS:
- has STRAIGHT CARBON CHAINS–attached to GLYCEROL, ESTER LINKAGE

FIRST AMINO ACID:
- METHIONINE (MET)

ANTIBIOTIC SENSITIVITY:
- X

rRNA LOOP:
- X

COMMON ARM of tRNA:
- YES

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14
Q

define ENDOSYMBIOTIC THEORY

A

based upon rRNA ANALYSIS:
ancestral cells of ARCHAEA and BACTERIA – eventually develops into EUKARYOTES

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15
Q

define SYMBIOSIS

A

SYMBIOSIS:
- “living together”

ex. CYANOPHORA PARADOXA
- both the EUKARYOTIC HOST and BACTERIUM require help from each other for survival
- bacteria makes their own food
- begins to supply the cell as well

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16
Q

what are the oldest known evidence of prokaryotes?

A

the oldest known fossils of PROKARYOTES were dated back over 3.5 BILLION YEARS AGO
- ex. CYANOBACTERIA like fossils found in rocks

17
Q

do we use FOSSIL EVIDENCE for prokaryotes a lot?

A

Not necessarily–fossil evidence of prokaryotes is extremely rare and NOT READILY AVAILABLE

PHYLOGENY:
- use and looking for SIMILARITIES in GENOMES
- use of rRNA SEQUENCING–very HIGHLY CONSERVED (few mutations)

18
Q

what is TAXONOMY based upon?

A

based on a HIERARCHY OF CLASSIFICATION
- the LOWER YOU GO, the MORE CLOSELY RELATED the LIVING THINGS ARE

19
Q

why do we need to identify microorganisms? (4)

A
  • AVOIDANCE OF FOOD POISONING OUTBREAKS
  • identifying INFECTIOUS AGENTS and help DETERMINE TREATMENT
  • AVOID FOOD SPOILAGE
  • AVOID ENVIRONMENTAL EXPOSURE
20
Q

what are some EXAMPLES of FOOD POISONING OUTBREAKS?

A
  1. GROUND BEEF (E. COLI O26)
    - affected multiple states
    - indication of SHIGA-LIKE TOXIN (causes diarrhea)
    - over 40 hospitalizations
  2. ROMAINE LETTUCE (E. COLI O157)
    - affected over 210 people in 36 states
    - over 96 hospitalizations / 5 deaths
  3. TURKEY (SALMONELLA)
    - affected multiple states; 90 people
    - over 6 hospitalizations / 1 death
21
Q

why is it important to IDENTIFY INFECTIOUS AGENTS?

A

can help to find out how ANTIBIOTICS WORK
- understanding the significance of ANTIBIOTIC RESISTANT BACTERIA

22
Q

why do we need to AVOID ENVIRONMENTAL EXPOSURE?

A

ex. brain-eating amoeba in lakes
- shows symptoms of fever, headache, nausea, or even confusion
- only 4 of the 157 people known to be infected have survived

23
Q

what are the METHODS of IDENTIFYING MICROORGANISMS (6)?

A

PHENOTYPIC METHODS:
- MORPHOLOGY
- STAINING
- BIOCHEMICAL TESTING
- MOTILITY

  • GENETIC AND MOLECULAR ANALYSIS
  • can also use BERGEY’S MANUAL as a reference book–helps for identification
24
Q

what are the TYPES OF STAINING?

A

GRAM STAIN:
- identification of the CELL WALL and specific PEPTIDOGLYCAN LAYER

ACID-FAST STAINING:
- stain binds to WAXY MATERIAL (Mycolic acid) in cell wall

CAPSULE STAINING
ENDOSPORE STAINING

25
Q

what are the types of METABOLIC and BIOCHEMICAL RXNS/TESTS?

A
  • tests that focus on GROWTH on SELECTIVE AND DIFFERENTIAL MEDIA
  • ex. fixing nitrogen
  • ex. oxidization of sulfur
  • ex. kind of carbon source
26
Q

describe SERLOGICAL METHODS

A

SERLOGICAL METHODS:
- use of HOST SERUM and IMMUNE RESPONSE that are present in the SERUM to identify MICROORGANISMS
**MICROORGANISMS are ANTIGENIC–respond by producing ANTIBODIES

what we are looking for:
- INTERACTION BETWEEN KNOWN ANTIBODIES and UNKNOWN BACTERIA–identify our unknown

ex. STREP QUICK TEST

27
Q

describe MOLECULAR METHODS

A

MOLECULAR METHODS:
- looking at the DNA of the microorganism
- not too practical to really sequence the WHOLE ENTIRE GENOME
- **identifying SPECIFIC DNA FRAGMENTS that are UNIQUE TO AN ORGANISM

METHODS:
1. DNA FINGERPRINTING
2. PCR

28
Q

describe method of DNA FINGERPRINTING

A

specific RESTRICTION ENZYMES cut DNA into FRAGMENTS OF DISTINCT SIZE
- can help IDENTIFY SPECIFIC PATTERN OF RESTRICTION of the bacteria–from here, we can IDENTIFY THE ORGANISM

29
Q

define and describe PCR

A

POLYMERASE CHAIN REACTION (PCR):
method to AMPLIFY a SEGMENT OF DNA by several order of magnitude

use of specific PRIMERS:
- little fragments of DNA that are specific to the GENE one is testing for
- can be GENERAL and AMPLIFY FAMILY OF GENES

30
Q

why is PCR so important?

A
  • one of the MOST IMPORTANT ADVANCES in molecular biology
  • important for GENETIC TESTING–looks for specific DISEASE CAUSING ORGANISM
  • creation of SPECIALIZED CANCER TREATMENT
31
Q

describe DNA MICROARRAY

A

method to help identify a pathogen by identifying a gene that is UNIQUE TO THAT PATHOGEN
- use of a grid microarray

MICROBIO BIOL-160 LEC (21 decks)

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