Microbiology 2

Question 1

what do biological systematics study?

Answer 1

how life changes through time and how living things relate to one another

Question 2

what is taxonomy?

Answer 2

defines systems by shared characteristics

Question 3

what is classification?

Answer 3

arrange organisms into groups

Question 4

what is nomenclature?

Answer 4

assigns names

Question 5

Linnaeus

Answer 5

1735
2 kingdoms
not described
vegetablia 
Animalia

Question 6

Haeckel

Answer 6

1866
3 kingdoms
protista 
plantae
Animalia

Question 7

Chatton

Answer 7

1925
2 empires
prokaryota
eukaryota

Question 8

Whittaker

Answer 8

1969
5 kingdoms
monera
protista 
plantae
fungi 
Animalia

Question 9

Woese

Answer 9

1977
3 kingdoms
bacteria
archaea
eukarya

Question 10

what are the 3 cellular entities?

Answer 10

• eukarya
• archaea
• bacteria

Question 11

what are the 2 acellular entities?

Answer 11

• prions

- viruses, viroids, virusoids

Question 12

viruses and prions are what type of entities?

Answer 12

anomalous

• non living
• viruses = parasitic

Question 13

what are the 2 competing systems for viral classification?

Answer 13

• Baltimore system

- international committee for taxonomy of viruses (ICTV) system

Question 14

what is viral classification based on?

Answer 14

• phenotype

- nucleic acid type

Question 15

properties of prions (PrP)?

Answer 15

• don’t reproduce
• misfolded proteins
• can exist as multiple isoforms

Question 16

what is a species?

Answer 16

group of living organisms capable of interbreeding, even if geographically isolated

Question 17

what is a species in microbiology?

Answer 17

collection of strains that share stable properties but differ significantly from other groups of strains

Question 18

what is a strain?

Answer 18

genetic variant / subtype of bacterial species that varies slightly from other members of same species

Question 19

what are organisms assigned on the basis of?

Answer 19

• phenotype
• serotype
• genotype

Question 20

phenotype?

Answer 20

organisms observable characteristics / traits e.g morphology, development, biochemical / physiological properties

Question 21

serotype?

Answer 21

distinct variations in cell surface antigens within species

Question 22

genotype?

Answer 22

part of genetic makeup of cell which determines one of its characteristics

Question 23

what does morphology include?

Answer 23

• cell shape (bacilli / cocci)

- cell structure (gram staining)

Question 24

what does biochemistry include?

Answer 24

• enzyme production

- transport proteins activity

Question 25

what does life cycle include?

Answer 25

vegetative / spore forming

Question 26

what does ecological niche include?

Answer 26

- temperature - thermophile - psychrophile

Question 27

what does interactions with other organisms include?

Answer 27

susceptibility to bacteriophages

Question 28

what does pathogenicity include?

Answer 28

ability to cause disease | provides least info

Question 29

salmonella genus has over how many different serotypes?

Answer 29

2600

Question 30

Kauffman-white classification

Answer 30

O antigen - oligosaccharides on cell surface H antigen - flagellar proteins

Question 31

vibrio cholera (cholera causing bacterium) has over how many serotypes?

Answer 31

200

Question 32

which 2 serotypes cause cholera? and what does it require?

Answer 32

O1 and O139 needs specific antibodies and pure cultures

Question 33

give examples of genomics?

Answer 33

- PCR - amplification of selected region of interest - base composition (%G/C) - nucleic acid sequencing: 16S rRNA - used in phylogenetic due to slow rate of evolution - also used in diagnosis - whole genome sequencing

Question 34

bacterial species definition?

Answer 34

genome sequences are at least 95% identical

Question 35

taxonomy base on genetics can be confused by what?

Answer 35

horizontal gene transfer

Question 36

what is vertical transmission?

Answer 36

passage of genetic info from parent to offspring

Question 37

what is horizontal transmission?

Answer 37

acquisition of genetic info by transfer from organism that is not parent

Question 38

what is whole genome sequencing?

Answer 38

determines complete DNA sequence of organism at single time

Question 39

how can we characterise the info we get from whole genome sequencing?

Answer 39

- presence/absence of genes: mecA gene in staphylococcus aureus - gene mutations: point mutations (SNPs) - can change protein encoding - gene insertions/deletions - acquired genes from horizontal transfer - phylogenetics

Question 40

what is phylogenetics?

Answer 40

study of evolutionary relationships among biological entities (in species)

Question 41

what do phylogenetics produce?

Answer 41

clusters (clades) of similar organisms based on DNA/protein sequences

Question 42

for 2/more sequences …. can be produced

Answer 42

multiple sequence alignments

Question 43

more closely related = ...

Answer 43

more similar genetic sequences

Question 44

what is MSA converted into?

Answer 44

- genetic distance (% similarity) | - summarises % similarity between each pair of sequences

Question 45

what do phylogenetic trees visualise?

Answer 45

evolutionary relationships between organisms

Question 46

what does rooted mean?

Answer 46

each node based upon inferred most recent ancestor

Question 47

what does unrooted mean?

Answer 47

only how each leaf relates to others (no inference on ancestry)

Question 48

what are microorganisms categorised by?

Answer 48

advisory committee on dangerous pathogens (ACDP) biosafety level (BSL)

Question 49

how many classification levels are there for the ACDP and BSL?

Answer 49

4

Question 50

what are pathogens classified on for ACDP?

Answer 50

severity of disease and availability of treatment

Question 51

what is being categorised for BSL?

Answer 51

facilities

Question 52

what is the general rule of thumb?

Answer 52

BSL > or equal to ACDP level

Question 53

ACDP category 1 organisms

Answer 53

- pose minimal levels of hazard to personnel/enviro - generally non-pathogenic e.g. B. subtilis, E. coli, saccharomyces cerevisiae

Question 54

BSL-1 facilities

Answer 54

- general protective equipment only - wash hands on entry and exit - sterilise all potentially infectious material

Question 55

ACDP category 2 organisms

Answer 55

- can cause human disease - may = hazardous to enviro - unlikely spread through local population - effective prophylaxis treatment / vaccination available e.g. staphylococcus aureus, pseudomonas aeruginosa, e.coli

Question 56

BSL-2 facilities

Answer 56

- all conditions for BSL-1 - highly regulated design and procedures - specific training - restricted access to lb - work can = performed in BSL cabinets

Question 57

ACDP category 3 organisms

Answer 57

- can cause severe human disease - may = severely hazardous to enviro - potential to spread through local population - effective prophylaxis, treatment / vaccination available e.g. B anthracis, mycobacterium tuberculosis, rabies virus some pathogens may need additional approvals

Question 58

BSL-3 facilities

Answer 58

- all conditions for BSL-1 and 2 - highly regulated design and procedures - all procedures done with BSL - lab specific PPE (or disposable) - under negative air pressure - all personnel offered vaccines

Question 59

ACDP category 4 organisms

Answer 59

- causes severe human disease (death) - severely hazardous to enviro - high risk of spread through local population - no treatment e.g. ebola, variola

Question 60

BSL-4 facilities

Answer 60

- all BSL 1,2,3 - personnel wear protective clothing - highly trained - highly regulated procedures - organisms handled carefully