Classifying and Identifying Microorganisms

Question 1

definition of TAXONOMY

Answer 1

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

Question 2

how does MODERN TAXONOMY differ now?

Answer 2

• 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

Question 3

describe TWO KINGDOM CLASSIFICATION

Answer 3

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

Question 4

what is the current system for DOMAINS?

Answer 4

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

Question 5

what was the TRADITIONAL FIVE-KINGDOM SYSTEM?

Answer 5

• MONERA
• PROTISTA
• PLANTAE
• FUNGI
• ANIMALIA

Question 6

what was the SIX-KINGDOM SYSTEM?

Answer 6

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

Question 7

definition of domain

Answer 7

the BROADEST TAXONOMIC GROUP

Question 8

definition of MODERN TAXONOMY

Answer 8

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

Question 9

definition of PHYLOGENY

Answer 9

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

Question 10

what is a PHYLOGENETIC TREE?

Answer 10

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

Question 11

describe some CHARACTERISTICS of ARCHAEA

Answer 11

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

Question 12

describe some CHARACTERISTICS of BACTERIA

Answer 12

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

Question 13

describe some CHARACTERISTICS of EUKARYA

Answer 13

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

Question 14

define ENDOSYMBIOTIC THEORY

Answer 14

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

Question 15

define SYMBIOSIS

Answer 15

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

Question 16

what are the oldest known evidence of prokaryotes?

Answer 16

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

Question 17

do we use FOSSIL EVIDENCE for prokaryotes a lot?

Answer 17

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)

Question 18

what is TAXONOMY based upon?

Answer 18

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

Question 19

why do we need to identify microorganisms? (4)

Answer 19

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

Question 20

what are some EXAMPLES of FOOD POISONING OUTBREAKS?

Answer 20

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

Question 21

why is it important to IDENTIFY INFECTIOUS AGENTS?

Answer 21

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

Question 22

why do we need to AVOID ENVIRONMENTAL EXPOSURE?

Answer 22

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

Question 23

what are the METHODS of IDENTIFYING MICROORGANISMS (6)?

Answer 23

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

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

Question 24

what are the TYPES OF STAINING?

Answer 24

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

Question 25

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

Answer 25

- tests that focus on GROWTH on SELECTIVE AND DIFFERENTIAL MEDIA - ex. fixing nitrogen - ex. oxidization of sulfur - ex. kind of carbon source

Question 26

describe SERLOGICAL METHODS

Answer 26

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

Question 27

describe MOLECULAR METHODS

Answer 27

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

Question 28

describe method of DNA FINGERPRINTING

Answer 28

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

Question 29

define and describe PCR

Answer 29

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

Question 30

why is PCR so important?

Answer 30

- one of the MOST IMPORTANT ADVANCES in molecular biology - important for GENETIC TESTING--looks for specific DISEASE CAUSING ORGANISM - creation of SPECIALIZED CANCER TREATMENT

Question 31

describe DNA MICROARRAY

Answer 31

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