Classifying and Identifying Microorganisms Flashcards
definition of TAXONOMY
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
how does MODERN TAXONOMY differ now?
- 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
describe TWO KINGDOM CLASSIFICATION
classified by CARL LINNAEUS in 1735
- classified under PLANTS and ANIMALS
what is the current system for DOMAINS?
CURRENT–THREE-DOMAIN-SYSTEM:
- BACTERIA (have prokaryotic cells)
- ARCHAEA (have prokaryotic cells)
- EUKARYA (have eukaryotic cells)
what was the TRADITIONAL FIVE-KINGDOM SYSTEM?
- MONERA
- PROTISTA
- PLANTAE
- FUNGI
- ANIMALIA
what was the SIX-KINGDOM SYSTEM?
- BACTERIA
- ARCHAEA
(part of the original “MONERA” system) - PROTISTA
- PLANTAE
- FUNGI
- ANIMALIA
definition of domain
the BROADEST TAXONOMIC GROUP
definition of MODERN TAXONOMY
MODERN TAXONOMT:
- reflects the PHYLOGENETIC RELATIONSHIP of organisms
- shows the EVOLUTIONARY RELATIONSHIP among various species
definition of PHYLOGENY
PHYLOGENY:
- the HISTORY of the EVOLUTION of a species or a group of organisms
- based on EVOLUTIONARY DEVELOPMENT
what is a PHYLOGENETIC TREE?
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
describe some CHARACTERISTICS of ARCHAEA
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
describe some CHARACTERISTICS of BACTERIA
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
describe some CHARACTERISTICS of EUKARYA
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
define ENDOSYMBIOTIC THEORY
based upon rRNA ANALYSIS:
ancestral cells of ARCHAEA and BACTERIA – eventually develops into EUKARYOTES
define SYMBIOSIS
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
what are the oldest known evidence of prokaryotes?
the oldest known fossils of PROKARYOTES were dated back over 3.5 BILLION YEARS AGO
- ex. CYANOBACTERIA like fossils found in rocks
do we use FOSSIL EVIDENCE for prokaryotes a lot?
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)
what is TAXONOMY based upon?
based on a HIERARCHY OF CLASSIFICATION
- the LOWER YOU GO, the MORE CLOSELY RELATED the LIVING THINGS ARE
why do we need to identify microorganisms? (4)
- AVOIDANCE OF FOOD POISONING OUTBREAKS
- identifying INFECTIOUS AGENTS and help DETERMINE TREATMENT
- AVOID FOOD SPOILAGE
- AVOID ENVIRONMENTAL EXPOSURE
what are some EXAMPLES of FOOD POISONING OUTBREAKS?
- GROUND BEEF (E. COLI O26)
- affected multiple states
- indication of SHIGA-LIKE TOXIN (causes diarrhea)
- over 40 hospitalizations - ROMAINE LETTUCE (E. COLI O157)
- affected over 210 people in 36 states
- over 96 hospitalizations / 5 deaths - TURKEY (SALMONELLA)
- affected multiple states; 90 people
- over 6 hospitalizations / 1 death
why is it important to IDENTIFY INFECTIOUS AGENTS?
can help to find out how ANTIBIOTICS WORK
- understanding the significance of ANTIBIOTIC RESISTANT BACTERIA
why do we need to AVOID ENVIRONMENTAL EXPOSURE?
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
what are the METHODS of IDENTIFYING MICROORGANISMS (6)?
PHENOTYPIC METHODS:
- MORPHOLOGY
- STAINING
- BIOCHEMICAL TESTING
- MOTILITY
- GENETIC AND MOLECULAR ANALYSIS
- can also use BERGEY’S MANUAL as a reference book–helps for identification
what are the TYPES OF STAINING?
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
what are the types of METABOLIC and BIOCHEMICAL RXNS/TESTS?
- tests that focus on GROWTH on SELECTIVE AND DIFFERENTIAL MEDIA
- ex. fixing nitrogen
- ex. oxidization of sulfur
- ex. kind of carbon source
describe SERLOGICAL METHODS
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
describe MOLECULAR METHODS
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
describe method of DNA FINGERPRINTING
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
define and describe PCR
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
why is PCR so important?
- one of the MOST IMPORTANT ADVANCES in molecular biology
- important for GENETIC TESTING–looks for specific DISEASE CAUSING ORGANISM
- creation of SPECIALIZED CANCER TREATMENT
describe DNA MICROARRAY
method to help identify a pathogen by identifying a gene that is UNIQUE TO THAT PATHOGEN
- use of a grid microarray
