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MBB163 - Microbiology > Dr Mesnage > Flashcards

Flashcards in Dr Mesnage Deck (109):
1

What are the three domains?

Bacteria, Archaea and Eukarya

2

How does genetic fluidity generate microbial diversity?

-Rapid multiplication (Binary fission)
-Haploid genome
-Horizontal gene transfer (Transduction and conjugation)

3

What is phylogeny?

The study of the evolutionary history of organisms

4

How does phylogeny work?

By comparing DNA sequences called molecular clocks

5

What do molecular clocks do?

Encode conserved proteins with similar functions

Undergo random and neutral mutations at a steady state

6

How are DNA sequences compared in phylogeny?

Measure divergence and construct phylogenetic trees (cladograms)

7

What is taxonomy?

The classification of organisms

8

What are the taxonomic subdivisions?

Domain -> Kingdom -> Phylum -> Class -> Order -> Family -> Genus -> Species

9

What are the methods of phenotypic analyses?

-Morphology/Differential staining
-Metabolic properties
-Phage typing
-Fatty acid profiles
-Mass spectrometry

10

What are the methods of genotypic analyses?

-DNA/DNA hybridisation (Gene differences)
-Fluorescence in situ hybridisation (FISH)
-rDNA (16S) sequencing
-Multi locus sequence typing/fingerprinting
-Whole genome sequencing

11

What are the two major differences between prokaryotic and eukaryotic cells?

Size and organelles/compartmentalisation

12

What is the functional anatomy of the nucleus in the eukaryotic cell?

-Contains chromatin

-Site of mRNA, tRNA and rRNA synthesis (rRNA in the nucleolus)

13

What is chromatin?

DNA complexed with histones

14

What is the functional anatomy of the rER in the eukaryotic cell?

-Membrane network covered with ribosomes
-Site of protein synthesis (outer face)
-Specific sorting signals allow import into rER
-Protein trafficking

15

What is the functional anatomy of the sER in the eukaryotic cell?

-No protein synthesis
-Contributes to lipid synthesis, steroids
-Toxin breakdown
-Protein trafficking

16

What is the functional anatomy of the Golgi complex in the eukaryotic cell?

-Carbohydrate synthesis (cells walls, extracellular matrix)

-Modification of proteins for specific targeting (secretion/incorporation in membranes)

17

What is the functional anatomy of the lysosomes in the eukaryotic cell?

-Originate from Golgi, can fuse with other vesicles

-Contain digestive enzymes to hydrolyse macromolecules

18

What is the functional anatomy of the peroxisomes in the eukaryotic cell?

-Originate from ER
-Incorporate lipids and proteins from cytoplasm
-Oxidise alcohols and fatty acids(role in lipid metabolism)

19

What is the functional anatomy of the mitochondria in the eukaryotic cell?

-Respiration
-Has its own DNA/translation machinery
-Multiply by division

20

What is the functional anatomy of the chloroplasts in the eukaryotic cell?

-Made of thylakoids (forming grana) found in stroma (matrix)
-Converts light into organic compounds via the Calvin cycle
-Has its own DNA/translation machinery
-Multiply by division

21

What is the functional anatomy of the flagella/cilia in the eukaryotic cell?

-Consists of a bundle of 9 pairs of microtubules surrounding central pair (axoneme)
-Microtubules connected via dynein molecules
-Motion driven by ATP hydrolysis by dynein
-Microtubules slide against one another, giving a whiplike movement

22

What is the functional anatomy of the nucleoid in the prokaryotic cell?

-Single, circular chromosome
-DNA complexed with histone-like proteins
-Genetic material also includes plasmids

23

What is the functional anatomy of the cytoplasm in the prokaryotic cell?

-Can contain organelles such as magnetosomes, photosynthetic membranes and internal membranes
-Contains proteins, tRNAs, mRNA and ribosomes
-Can contain protein bound inclusion bodies like carboxysomes, storage granules and gas vesicles

24

What is the functional anatomy of the envelope in the prokaryotic cell?

Cytoplasmic membrane, peptidoglycan with polymers bound to it and outer membrane

25

What is the functional anatomy of the pilus in the prokaryotic cell?

Appendage dedicated to conjugation (plasmid exchange)

26

What is the functional anatomy of the fimbriae (pili) in the prokaryotic cell?

-Involved in adherence to host cells/surfaces

-Antigenic structures made of 1 major protein

27

What is the functional anatomy of the flagella in the prokaryotic cell?

Supramolecular assembly involved in bacterial motility

28

What is thought to be the endosymbiotic origin of eukaryotes?

-Mitochondria originated from engulfment of a hydrogen-producing bacterium by a hydrogen-consuming Archae
-Genes for lipid synthesis were transferred to host, giving rise to the nucleus
-Chloroplasts were acquired later by endosymbiosis

29

What are the general properties of viruses?

-Obligatory parasites
-Small
-Made of a nucleic acid genome surrounded by a protein coat (capsid) and a facultative lipid membrane(envelope)
-Viruses exist that can infect all living organisms

30

What is the genome composition of the nucleic acid of viruses?

-DNA; ss or ds

-RNA; ss(+/-) or ds

31

What is the size of the nucleic acid of viruses?

-Small; minimal info; only specific genes

-ds>ss; DNA>RNA

32

What is the organisation of the nucleic acid of viruses?

Usually 1 molecule, can be fragmented

33

What are the properties of the capsid of viruses?

-Made of proteins called capsomers

-Self assembly products; highly ordered

34

What are the properties of the envelope of viruses?

-Made of a lipid bilayer with (glyco)proteins from host or virus-encoded

-allows entry into host cell (fusion/endocytosis)

35

What are the properties of bacteriophages?

Contain a mixture of icosahedral/filamentous structures (+others)

36

What is the Baltimore classification?

-Group 1, 2 and 7: DNA viruses

-Group 3, 4, 5, 6: RNA viruses

37

What is the life cycle for bacteriophages?

Lytic and lysogenic cycles

38

What is the life cycle for animal/plant viruses?

-Attachment
-Penetration
-Biosynthesis
-Maturation
-Release

39

What are the common bacterial morphologies?

-Cocci (Spherical)
-Rods
-Curved
-Spiral
-Exotic (Others)

40

Why are bacteria often appear coloured?

They produce pigments

41

What is the method for Gram staining?

-Stain with crystal violet
-Fix with iodine
-Wash with alcohol
-Counter stain with safranin

42

What colour are Gram-positive bacteria stained?

Purple

43

What are the properties of capsules in bacteria?

-Most made of polysaccharides, some made of amino acids
-Covalently bound to cell wall or outer membrane
-Confer resistance to host phagocytes/bacteriophages
-Keep environment hydrated

44

What are the properties of exopolysaccharides in bacteria?

-Non-covalently attached to the cell surface
-Important for biofilm formation
-Some are economically important

45

What are the properties of S-layers in bacteria?

-Facultative structures
-Non-covalently bound to the cell surface
-Proteinaceous crystalline arrays; self assembly products
-Uncommon in model organisms

46

What are the properties of the outer membrane in gram negative bacteria?

-Phospholipids
-Proteins including porins
-Lipoproteins covalently linked to peptidoglycan
-LPS: Activator of the immune system

47

What are the properties of peptidoglycan in bacteria?

-Glycan chain
-Cell shape exoskeleton
-Regulates exchanges with the environment
-Scaffold for the display of polymers and proteins

48

What are the properties of cytoplasmic membrane in bacteria?

-Phospholipids (Modulate fluidity and permeability)
-Hopanoids (Modulate fluidity and permeability)
-Proteins (Ion, proteins or nutrient transport)

49

What are the properties of the chromosome in bacteria?

-Made of dsDNA
-Normally a single circular chromosome
-Organised as a nucleoid

50

What are the properties of the plasmids in bacteria?

-Always dsDNA, usually circular
-Variable copy number
-Can be (self)-transferable
-Carry resistance genes

51

What are the properties of the gene structure in bacteria?

-No introns

-Operons: one promoter and several ORFs

52

What is the method of transcription initiation in bacteria?

-RNA Polymerase scans DNA forming a loose complex
-Sigma factor binds to -35 and -10 sequences upstream of start codon (Closed complex)
-DNA unwinds forming open complex, transcription starts and sigma factor released

53

What is the method of rho-independent transcription termination in bacteria?

Palindromic G-C rich region upstream of A-T rich region transcribed, forming a hairpin loop structure that makes the RNApol to fall apart, helped by the A-T rich region as it has few hydrogen bonds

54

What is the method of rho-dependent transcription termination in bacteria?

-Rho protein recognises and binds to 72 G-C rich area on RNA
-Rho wraps the downstream around itself, due to its RNA-dependent ATPase activity
-Once it reaches the polymerase, Rho unwinds the RNA-DNA duplex, releasing the polyymerase

55

What are the five major parameters important for bacterial growth?

-Temperature
-pH
-Osmotic pressure
-Nutrients
-Oxygen

56

What occurs at the minimum temperature for bacterial growth?

Membrane gelling; transport processes so slow that growth cannot occur

57

What occurs at the maximum temperature for bacterial growth?

Protein denaturation; collapse of the cytoplasmic membrane; thermal lysis

58

What are psychrophiles?

Bacteria that grow at very low temperatures (Between 0 and 20C)
-E.g. P. vacuolata

59

What are mesophiles?

Bacteria that grow at standard temperatures (Between 12 and 43C)
-E.g. E. coli

60

How are psychrophiles adapted to cold temperatures?

-Increased membrane fluidity by more unsaturated fatty acids
-Production of anti-freeze proteins and cryoprotectants
-Production of cold adapted enzymes

61

How are thermophiles adapted to high temperatures?

-Genome protection by DNA-binding proteins, supercoils and high G-C%
-Modification of the membrane composition
-Production of thermostable proteins
-Existence of thermostable chaperonins

62

How is the metabolism of alkaliphiles adapted?

-Pumping of Na+ (Decarboxylases and respiratory chains)
-Na+ motive force drives substrate transport and motility
-Na+ drives ATP synthesis
-Antiporters scavenge protons

63

How is the metabolism of acidophiles adapted?

-K+/H+ antiporters and respiratory chains remove H+
-H+ motive force drives substrate transport and motility
-H+ drives ATP synthesis
-H+/Na+ antiporters maintain pH

64

What are the different classes of bacteria with regard to their osmotic conditions?

-Nonhalophile
-Halotolerant
-Halophile
-Extreme halophile

65

How are bacteria adapted to osmotic conditions?

-Regulation of water movement
-Production of and release of compatible solutes

66

What are the Reactive Oxygen Species (ROS)?

-Superoxide ([O2]-)
-Hydrogen peroxide
-Hydroxyl radical

67

What are the enzymes that detoxify ROS?

-Catalase/peroxidase
-Superoxide dismutase (SOD) + Catalase
-Superoxide reductase (SOR) + Catalase

68

What is the effect of Catalase/peroxidase with regards to their detoxification of ROS?

Convert hydrogen peroxide to water

69

What is the effect of Superoxide dismutase + Catalase with regards to their detoxification of ROS?

Convert superoxide to hydrogen peroxide then water

70

What is the effect of Superoxide reductase + Catalase with regards to their detoxification of ROS?

Convert superoxide to hydrogen peroxide then water

71

What are the oxygen requirements of Obligate aerobes?

-Use Catalase + SOD
-Use only oxygen for respiration

72

What are the oxygen requirements of Facultative aerobes?

-Use Catalase + SOD
-Can use oxygen for respiration

73

What are the direct measurement methods of measuring bacterial growth?

-Microscopic counts
-Viable counting
-Flow cytometry

74

What are the indirect measurement methods of measuring bacterial growth?

-Optical density
-Dry weight
-Metabolic activity

75

What are the limitations to using optical density for measuring bacterial growth?

-Requires high cell densities
-Does not distinguish between lie and dead cells
-OD values differ depending on organisms
-Does not work with moulds and filamentous bacteria

76

What are the two major phyla of Archaea?

-Euryarcheota

-Crenarcheaota

77

What are the properties of the S-layer in archaea?

-Outermost structure
-Composed of a 2D crystalline array of (glyco)proteins
-May have a role in cell shape

78

What are the properties of the cell wall in Archaea?

-Pseudomurein
-Not always present
-Heteropolymer (disaccharide peptides)
-Resistant to lysozyme and most antibiotics targeting bacterial peptidoglycan synthesis

79

What are the properties of the cytoplasmic membrane in archaea?

-Phospholipids contain isoprenes not fatty acids
-Phospholipids are ether- not ester-linked
-Present as monolayers or bilayers (or a mixture)

80

What are the properties of chromosome organisation and replication in archaea?

-Circular chromosome & plasmids
-Histones
-Multiple replication origins
-Encode polymerase B and D (D is specific to Archaea)

81

What are the properties of transcription and RNA processing in archaea?

-Only one RNA pol
-Presence of introns
-Genes organised in operons

82

What are the properties of translation in archaea?

-Coupled to transcription
-Involves several translation factors
-70S ribosomes

83

What are the properties of archaea (Hyper)thermophiles?

-Include Crenarchaeota and Euryarchaeota
-High growth temperature
-Most require elemental sulfur for growth
-Often acidophiles

84

What are the properties of archaea halophiles?

-Mostly euryarchaeota
-Found in evaporating ponds, salty lakes
-Require up to 5M NaCl for growth

85

What are the properties of archaea methanogens?

-Euryarchaeota
-Found in anaerobic environments
-Use acetate/formiate/CO2 as electron acceptor

86

What are the 3 physical methods used to eradicate bacteria?

-Heat
-Irradiation
-Filtration

87

What is the difference between bactericidal and bacteriostatic agents?

Bactericidal stop growth by killing the bacteria while bacteriostatic just stop growth

88

What is the mode of action of B-lactams?

Inhibit peptidoglycan polymerisation mediated by D, D-transpeptidases

89

What are the 4 mechanisms conferring resistance to B-lactams?

-Inactivation by B-lactamases
-Mutation of the target enzyme
-Secretion of the antibiotic (Gram -ve bacteria)
-Modification of the synthetic pathway targeted by B-lactams

90

What is the thermal death point?

Minimum temperature at which all organisms are killed in 10 min in a particular liquid

91

What is the thermal death time?

Minimal time required to kill all bacteria in a particular liquid at a given temperature

92

What are the methods of using heating for antimicrobial control?

-Moist heat (Boiling heat/autoclave)
-Dry heat (Oven)
-Pasteurisation

93

What are the methods of using irradiation for antimicrobial control?

-Ionising radiation

Non-ionising radiation

94

How is filtration used for antimicrobial control?

-Used to sterilise gases or liquids that can be damaged by heat
-Porosity of filters can be chosen for specific applications

95

What are the main classes of chemical agents used for antimicrobial control?

-Sterilants
-Disinfectants
-Antiseptics and germicides

96

How are sterilants used for antimicrobial control?

-Used to destroy microorganisms on objects
-Completely eliminate or destroy all forms of microorganisms, including spores

97

How are disinfectants used for antimicrobial control?

-Used to destroy microorganisms on objects
-Kill microorganisms, but not necessarily endospores

98

How are antiseptics & germicides used for antimicrobial control?

Applied on living tissues and inhibit growth or kill microorganisms

99

What are the methods used to measure antimicrobial activity?

-Disc diffusion technique
-Minimum Inhibitory Concentration (MIC)
-Minimum Bactericidal Concentration (MBC)

100

What is the Minimum Inhibitory Concentration?

The lowest concentration of a drug inhibiting the visible growth of a test organism after overnight incubation

101

What is the Minimum Bactericidal Concentration?

The lowest concentration of a drug killing >99.9% of a test organism after overnight incubation

102

What are the chemicals used for antimicrobial control?

-Phenolic compounds
-Alcohols
-Aldehydes
-Quaternary ammonium compounds
-Halogen releasing agents

103

What are the antimicrobial effects of phenolic compounds?

Disrupt cytoplasmic membrane and denature proteins

104

What are the antimicrobial effects of alcohols?

Denature proteins; lipid solvent, disrupting cytoplasmic membrane

105

What are the antimicrobial effects of aldehydes?

Alkylating agents; modify proteins and DNA causing cell death

106

What are the antimicrobial effects of quaternary ammonium compounds?

Interact with phospholipids of the cytoplasmic membrane

107

What are the antimicrobial effects of chlorine-releasing agents?

Formation of chlorinated bases in DNA; oxidation of proteins

108

What are the antimicrobial effects of iodine-releasing agents?

Target DNA and proteins

109

What are the properties of an ideal antibiotic?

-Selective toxicity and inhibits an essential process
-Stable and effective
-Cheap