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PHA112 > Microbiology 2 > Flashcards

Microbiology 2 Flashcards

1
Q

what do biological systematics study?

A

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

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2
Q

what is taxonomy?

A

defines systems by shared characteristics

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3
Q

what is classification?

A

arrange organisms into groups

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4
Q

what is nomenclature?

A

assigns names

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5
Q

Linnaeus

A 
1735
2 kingdoms
not described
vegetablia 
Animalia
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6
Q

Haeckel

A 
1866
3 kingdoms
protista 
plantae
Animalia
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7
Q

Chatton

A

1925
2 empires
prokaryota
eukaryota

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8
Q

Whittaker

A 
1969
5 kingdoms
monera
protista 
plantae
fungi 
Animalia
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9
Q

Woese

A 
1977
3 kingdoms
bacteria
archaea
eukarya
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10
Q

what are the 3 cellular entities?

A
  • eukarya
  • archaea
  • bacteria
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11
Q

what are the 2 acellular entities?

A
  • prions

- viruses, viroids, virusoids

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12
Q

viruses and prions are what type of entities?

A

anomalous

  • non living
  • viruses = parasitic
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13
Q

what are the 2 competing systems for viral classification?

A
  • Baltimore system

- international committee for taxonomy of viruses (ICTV) system

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14
Q

what is viral classification based on?

A
  • phenotype

- nucleic acid type

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15
Q

properties of prions (PrP)?

A
  • don’t reproduce
  • misfolded proteins
  • can exist as multiple isoforms
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16
Q

what is a species?

A

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

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17
Q

what is a species in microbiology?

A

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

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18
Q

what is a strain?

A

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

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19
Q

what are organisms assigned on the basis of?

A
  • phenotype
  • serotype
  • genotype
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20
Q

phenotype?

A

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

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21
Q

serotype?

A

distinct variations in cell surface antigens within species

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22
Q

genotype?

A

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

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23
Q

what does morphology include?

A
  • cell shape (bacilli / cocci)

- cell structure (gram staining)

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24
Q

what does biochemistry include?

A
  • enzyme production

- transport proteins activity

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25
Q

what does life cycle include?

A

vegetative / spore forming

26
Q

what does ecological niche include?

A
  • temperature
  • thermophile
  • psychrophile
27
Q

what does interactions with other organisms include?

A

susceptibility to bacteriophages

28
Q

what does pathogenicity include?

A

ability to cause disease

provides least info

29
Q

salmonella genus has over how many different serotypes?

A

2600

30
Q

Kauffman-white classification

A

O antigen - oligosaccharides on cell surface

H antigen - flagellar proteins

31
Q

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

A

200

32
Q

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

A

O1 and O139

needs specific antibodies and pure cultures

33
Q

give examples of genomics?

A
  • 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
34
Q

bacterial species definition?

A

genome sequences are at least 95% identical

35
Q

taxonomy base on genetics can be confused by what?

A

horizontal gene transfer

36
Q

what is vertical transmission?

A

passage of genetic info from parent to offspring

37
Q

what is horizontal transmission?

A

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

38
Q

what is whole genome sequencing?

A

determines complete DNA sequence of organism at single time

39
Q

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

A
  • 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
40
Q

what is phylogenetics?

A

study of evolutionary relationships among biological entities (in species)

41
Q

what do phylogenetics produce?

A

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

42
Q

for 2/more sequences …. can be produced

A

multiple sequence alignments

43
Q

more closely related = …

A

more similar genetic sequences

44
Q

what is MSA converted into?

A
  • genetic distance (% similarity)

- summarises % similarity between each pair of sequences

45
Q

what do phylogenetic trees visualise?

A

evolutionary relationships between organisms

46
Q

what does rooted mean?

A

each node based upon inferred most recent ancestor

47
Q

what does unrooted mean?

A

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

48
Q

what are microorganisms categorised by?

A

advisory committee on dangerous pathogens (ACDP)

biosafety level (BSL)

49
Q

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

A

4

50
Q

what are pathogens classified on for ACDP?

A

severity of disease and availability of treatment

51
Q

what is being categorised for BSL?

A

facilities

52
Q

what is the general rule of thumb?

A

BSL > or equal to ACDP level

53
Q

ACDP category 1 organisms

A
  • pose minimal levels of hazard to personnel/enviro
  • generally non-pathogenic

e.g. B. subtilis, E. coli, saccharomyces cerevisiae

54
Q

BSL-1 facilities

A
  • general protective equipment only
  • wash hands on entry and exit
  • sterilise all potentially infectious material
55
Q

ACDP category 2 organisms

A
  • 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

56
Q

BSL-2 facilities

A
  • all conditions for BSL-1
  • highly regulated design and procedures
  • specific training
  • restricted access to lb
  • work can = performed in BSL cabinets
57
Q

ACDP category 3 organisms

A
  • 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

58
Q

BSL-3 facilities

A
  • 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
59
Q

ACDP category 4 organisms

A
  • causes severe human disease (death)
  • severely hazardous to enviro
  • high risk of spread through local population
  • no treatment

e.g. ebola, variola

60
Q

BSL-4 facilities

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

PHA112 (37 decks)

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