8. Classification of Prokaryotes

Question 1

Prokaryote classification - 2 reasons for importance?

Answer 1

• Understand evolutionary relatedness of modern organisms

- Allows us to predict characteristics of newly discovered organisms

Question 2

Difference between phenetic and phylogenetic classification?

Answer 2

Phenetic - based on phenotypic characteristics (observed, morphology)

Phylogenetic - based on molecular sequences -> evolutionary relatedness

Question 3

Phenetic classification - 3 characteristics examined?

Answer 3

Morphology (coccus/rod/vibrio)

Biochemistry (O2 requirements, carbon source)

Habitat (anaerobic sediments, gut of animals)

Question 4

Definition of “species” in higher organisms vs in bacteria?

Answer 4

Higher - reproductively isolated group that can produce viable offspring

Bacteria - asexual reproduction, fairly arbitrarily defined

Question 5

2 organisms are considered to be the same species if they share ____________

Answer 5

> 80% of their characteristics

Question 6

How similar are C.botulinum and C.sporogenes? What’s their main difference?

Answer 6

> 95% of their characteristics

C.botulinum produce the botulinum toxin, those that don’t are C.sporogenes

Question 7

Botulinum toxin is _____ times more toxic than snake venome

Answer 7

6 million

Question 8

3 different ways strains within a species can be termed?

Answer 8

Morphovar (differ in morphology)

Serovar (differ in response to antibiotics)

Biovar (differ in biochemical properties)

Question 9

System used in naming microorganisms is called the _______ system of Linnaeus

Answer 9

binomial

Question 10

How to quantify extent of similarity between microbes for phenetic information?

Answer 10

Use numerical taxonomy

Question 11

Numerical taxonomy -> how to accomplish?

Answer 11

Build a MATRIX of pair-wise comparisons between 2+ organisms and determine a SIMILARITY COEFFICIENT

Question 12

For numerical taxonomy, how many traits must be examined? Are all traits given the same weighting?

Answer 12

50 to several hundred traits

Yes - same weighting

Question 13

Numerical taxonomy - the matrix generates ________

Answer 13

an S-value

Question 14

What are the 2 types of S-coefficients? Differences?

Answer 14

S(SM) = simple matching coefficient

S(J) = Jaccard coefficient

S(SM) takes into account ALL traits, even if absent in both strains.

S(J) ignores traits that are absent in both strains

Question 15

S-values are ALWAYS between ___ and ___

Answer 15

0 and 1

Question 16

When 2 organisms are compared, the results can be depicted __________

Answer 16

graphically

Question 17

Botulinum toxin acts at ________________ junctions to block __________ release, leading to paralysis and death

Answer 17

at neuro-muscular junctions

block neurotransmitter release

Question 18

Dendogram ______ gives S-value for the pair of organisms

Answer 18

nodes

Question 19

3 ways protein structure can be used to measure relatedness?

Answer 19

3D shape - reactivity with specific antibodies

Protein amino acid sequence

Whole cell protein profiles - fingerprint of total proteins to quantify similarities

Question 20

Within a genus, %GC is within ____%

Answer 20

10%

Question 21

GC content is determined by _______________

Answer 21

melting temperature

Question 22

What type of method for measuring relatedness using molecular data uses conserved sequences such as rRNA genes

Answer 22

Nucleic acid content/sequence (genome)

Question 23

________________ is responsible for splitting bacteria and archaea

Answer 23

rRNA sequences

Question 24

Compared to bacteria, archaea cell walls do not contain ___________ or _____________

Answer 24

peptidoglycan or glycoproteins

Question 25

Difference between bacteria and archaea membrane lipids?

Answer 25

Archaea fatty acids are linked to the glycerol as ETHER rather than ester-linked

Question 26

Unique feature of archaea other than cell walls and membrane lipids?

Answer 26

Different RNA polymerase and tRNA structures

Question 27

Unique feature of archaea other than cell walls and membrane lipids?

Answer 27

Different RNA polymerase and tRNA structures

Question 28

3 methods that allow for strain identification (other than genome sequencing)?

Answer 28

Multilocus sequence typting Whole cell protein profiling Genomic fingerprinting

Question 29

2 methods that allow for family and genus identification?

Answer 29

Genome sequencing, 16S rDNA sequencing

Question 30

4 methods for measuring relatedness using molecular data?

Answer 30

1. Protein structure 2. Nucleic acid content 3. Whole genome sequencing 4. DNA-DNA hybridization

Question 31

No horizontal gene transfer is seen in ___________

Answer 31

16S rRNA sequences