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Bacteria Flashcards

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1
Q

what are the different bacterial morphologies?

A
  1. cocci
  2. rods
  3. curved
  4. spiral
  5. exotic - star-shaped cells
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2
Q

what is the cocci morphology of bacteria?

A
  • simplest, round-shaped cells
  • cell machinery at septum for elongation
  • some form pairs = diplococci
  • some form chains = streptococci
  • division planes can be parallel or perpendicular
  • form complex organisations like tetrads, sarcinae (multiple perpendicular divisions
  • can form microcolonies (piles of cells)
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3
Q

what is the rod morphology of bacteria?

A
  • elongated cells
  • bacilli = 1 rod
  • diplobacilli = 2 rods
  • multiple chains of rods = streptobacilli
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4
Q

what is the name given to a bacteria with a mixture of round cocci and rods?

A

coccobacilli

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5
Q

what is the curved morphology of bacteria?

A
  • governed by cytoskeleton proteins to create curved shape

- asymmetrical growth is maintained

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6
Q

what is the spiral morphology of bacteria?

A

spirillum:

  • cell shape adapted to organism lifestyle
  • helps bacteria move as a corkscrew and penetrate into mucus of epithelial cells
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7
Q

how can bacterial morphologies change during the cell cycle?

A
  1. in aquatic environment it forms swarmer cells - has flagella so can swim
  2. during life cycle, forms a stalk appendage so bacteria can adhere to surfaces
  3. as stalk grows, they divide asymmetricaly
  4. produce mobile form (swim) and immobile form (adhere)
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8
Q

what is the advantage of bacteria being small?

A

large SA:V ratio

  • increases nutrient exchange and growth rate
  • higher intracellular nutrient concentration
  • rapid evolution due to high selection rate of mutations and faster divisions
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9
Q

why do bacteria appear to be different colours?

A
  • they themselves aren’t coloured
  • they produce pigments as colonies
  • pigments fulfil roles in bacterial life cycles
  1. Prodigiosin = immunosuppressant
  2. staphyloaxanthin and violacein = antioxidant, detoxify ROS
  3. pyocyanin = cytotoxicity, neutrophil apoptosis, proinflammatory
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10
Q

why do bacteria have odours?

A
  • they form biproducts from metabolism which aren’t necessity for life, but do produce odour
  1. contribution to human odours via degragation of aprocrine products
    - conversion of leucine to isovaleric acid by Staph
    - production of propanoic acid by propionibacteria
  2. decarboxylation of amino acids to form polyamines
    - putrescine, spermidine, cadaverine have role is ROS and signalling
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11
Q

what is the gram staining process?

A
  1. colony sample spread onto glass slide and stained with crystal violet, which is +ve charge and penetrates cell envelope
  2. iodine solution, -ve charge, penetrates cell envelope, and allows crystal violet to form large complexes
  3. crystal violet is either stuck in envelope or washed off
  4. counter stain safranin is applied and stains cells that had crystal violet washed off
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12
Q

what is gram positive in the gram stain?

A
  • These bacteria retain methyl violet in their thick peptidoglycan cell walls
  • contain no outer membrane
  • Examples of Gram-positive bacteria are
    Staphylococcus and Streptococcus
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13
Q

what is gram negative in the gram stain?

A
  • These bacteria have only thin peptidoglycan cell walls
  • contain an outer membrane
    -Gram negative bacteria therefore appear pink-red. - Examples of Gram-negative
    bacteria are Escherichia, Pseudomonas and Neisseria
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14
Q

what bacteria does the gram stain not work on?

A

Mycobacteria

- has a unique cell envelope composition where the lipids interfere with the staining process

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15
Q

what are S-layers?

A
  • found in gram +ve and -ve
  • non-covalently bound to cell surface- - facultative (don’t exist in most model organisms)
  • proteinaceous crystalline arrays - self assembly products
  • 20% of bacterial production
  • not all bacteria have them
  • function unknown
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16
Q

what are capsules?

A
  • found in gram +ve and -ve
  • made of polysaccharide
  • some made of amino acids (poly-gamma-D-glutamate)
  • covalently bound to peptidoglycan (gram +ve) or outer membrane (gram -ve)
  • resistannt to phagocytes and bacteriophages
  • keep environment hydrated
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17
Q

what are exopolysaccharides?

A
  • homo- or heteropolysaccharides
  • non-covalently bound to cell surface
  • important for biofilm formation
  • form aggregates to protect fom environment
  • enables formation of colonies
  • economic importance: xanthan gum
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18
Q

what are the key components of the outer membrane in gram negative bacteria?

A
  • phospholipid bilayer
  • innerface = phospholipids
  • outerface = lipopolysaccharide, contains hydrophobic region
  • variable-O-antigen polysaccharide determines antigen on cell surface
  • contains porins for solute transport
  • lipoproteins are covalently linked to peptidoglycan
  • LPS endotoxin is a potent activator of the immune system: can trigger inflammation
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19
Q

what is peptidoglycan?

A
  • made of murein
  • maintains cell shape and forms exoskeleton
  • acts as scaffold to display proteins
  • protective role
  • acts as a sieve to regulate dynamic exchanges with environment
  • elastic 3D network
  • present in almost all bacteria
  • resistant to osmotic stress
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20
Q

what is the composition of peptidoglycan?

A
  • made of murein
  • glycan chains alternating N-acetylglucosamine G and N-acetylmuramic acid
  • substituted via short peptides (L and D amino acids)
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21
Q

how is peptidoglycan assembled?

A
  • transpeptidation reaction with enzymes which are covalently bound to the stem
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22
Q

what are the key components of the cytoplasmic membrane?

A
  • phospholipid bilayer
  • unsaturated fatty acids modulate membrane fluidity and permeability due to kinks in hydrocarbon chain
  • amphipathic molecules for compartmentalisation
  • hopanoids modulate membrane fluidity and permeability
  • protein transporters make membrane selectively permeable for specific polar molecules
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23
Q

what is the bacterial chromosome made up of?

A
  • dsDNA
  • singular, circular chromosome
  • 0.5-14.8mbp
  • organised as a nucleoid: histone-like proteins enable supercoiling
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24
Q

what is the bacterial plasmid made up of?

A
  • dsDNA
  • variable copy number
  • 2-600kbp
  • self-transferable by horizontal transfer
  • conjugation: physical contact between bacteria to transfer plasmid DNA
  • carry resistance genes
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25
Q

what is the gene structure of bacteria?

A
  • no introns
  • continuous coding sequence via open reading frame (ORF)
  • operons: one promoter, several ORFs
  • genes are smaller than eukaryotic genes
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26
Q

how is gene transcription initiated?

A
  1. RNAP scans DNA forming a loose complex
  2. sigma factor binds to shine-dalgarno sequence upstream of start codon (-35 and -10)
  3. DNA is unwound to form an open complex
  4. transcription begins and sigma factor is released
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27
Q

what is rho-independent transcription termination?

A
  1. requires palindromic GC-rich region upstream of an AT-rich sequence
  2. once the GC-rich region has been transcribed, it forms a hairpin
  3. hairpin causes dissociation of RNAP, helped by the AT-rich sequence (few H-bonds)
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28
Q

what is rho-dependent transcription termination?

A
  1. rho proteins recognise and bind to 72 GC-rich residues
  2. RNA-dependent ATPase wraps the downstream RNA around itself
  3. once it reaches the polymerase, rho unwinds the RNA-DNA heteroduplex and releases RNAP
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29
Q

how is the genetic machinery different between prokaryotes and eukaryotes?

A
  • transcription site is cytoplasm for bacteria (nucleus for eukaryotes)
  • 1 RNAP in bacteria, 3 RNAP eukaryotes
  • termination involves palindromic GC-rich region (eukaryotes require AAUAAA)
  • mRNA is modified in eukaryotes, but not in bacteria
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30
Q

how large are the ribosomes in bacteria compared to eukaryotes?

A

70S in bacteria
- 50S + 30S

80S in eukaryotes
- 60S + 40S

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31
Q

what are the differences in translation between bacteria and eukaryotes?

A
  • bacterial 70S ribosomes interact with mRNA productively in presence of tRNA
  • 30S subunit recognises SD sequence
  • transcription and translation are coupled in bacteria
  • eukaryotic 80s ribosomes bind mRNA efficiently in absence of tRNA
  • 40S subunit is guided by 5’ cap on mRNA
  • compartmentalised in eukarytoes
  • translation inhibited by cycloheximide
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32
Q

what does bacterial growth require?

A
  • temperature
  • pH
  • osmotic pressure
  • nutrients
  • oxygen
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33
Q

what are the cardinal temperatures for bacteria?

A

Minimum: below this, no growth ca occur as the membranes gel and transport processes are too slow to maintain metabolism

Optimum: an increased enzymatic activity so that reactions occur at the maximal possible rate

Maximum: after this point, proteins become denatured, cytoplasm collapses and cell lysis occurs, causing metabolic reactions to halt

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34
Q

name 4 bacteria and their optimal temperatures:

A
  1. P. vacuolata = 4C
    - psychrophile
  2. E. coli = 37C
    - mesophile
  3. T. aquaticus = 70C
    - thermophile
  4. P. fumarii = 106C
    - extreme thermophile
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35
Q

how are psychrophiles adapted to cold temperatures?

A
  1. increased membrane fluidity
    - more unsaturated and polyunsaturated methyl-branched fatty acids
    - limit membrane cohesion
  2. production of anti-freeze proteins
    - AFPs bind to ice crystals to inhibit their growth by covering water-accessible surfaces of ice
  3. production of cryoprotectants
    - trehalose and exopolysaccharides lowers freezing temp of water to preserve fluids
  4. production of cold-adapted enzymes
    - more a-helices and less weak bonds to combat low enthalpy
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36
Q

how are thermophiles adapted to high temperatures?

A
  1. genome protection
    - by DNA-binding proteins stabilise DNA
    - reverse DNA genes form supercoils - harder to pull apart
    - high GC% - difficult to denature
  2. modify membrane composition
    - stable ether-linked phosolipids
    - single lipid layer: glycerol tetraethers
  3. thermostable proteins
    - more ionic and hydrophobic interactions to form stronger bonds
  4. thermostable chaperonins
    - maintain protein folding
    - thermosome in Pyrodictium abyssi
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37
Q

how are acidophile metabolisms adapted to their environment?

A
  • increased membrane impermeability
  • use protons as currency
  • ATP depends on oxidative phosphorylation and needs H+ for this
  • use H+ to import/export Na+
  • H+ powers motility: when pumped in, H+ triggers conformational change to move flagella
  • H+ secretion systems via antiporters
  • DNA/protein repar mechanisms
  • reverse membrane potential and increased osmolarity (K+ ions)
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38
Q

how are alkaliphile metabolisms adapted to their environment?

A
  • Na+ as currency
  • use Na+ to make ATP
  • used for motility, imports/exports etc
  • high affinity transporters for Na+
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39
Q

how are bacteria adapted to osmotic stress?

A
  • regulate water movements by passive diffusion and aquaporins
  • produce compatible solutes like proline, glutamic acid and betaine
  • release solutes via mechano-sensitive channels
  • halophiles accumulate osmolites in their cytoplasm
40
Q

what are halophiles?

A
  • require high salt conc to grow

- S-layer is stabilised by Na+ ions, and K+ must be >4M in the cell

41
Q

what are non-halophiles?

A

cannot be exposed to high salt conc

42
Q

what are halotolerant bacteria?

A

can deal with high osmotic pressure by high salt conc, but to an extent

43
Q

what are extreme halophiles?

A
  • usually archaea

- need high salt conc

44
Q

what nutrients do bacteria require?

A
  • nitrogen
  • sulphur
  • phosphorus
  • vitamins
  • K+, Ca2+, Mg2+ (cofactors)
  • trace elements (Fe, Cu, Zn)
45
Q

what nutrients do bacteria require?

A
  • nitrogen
  • sulphur
  • phosphorus
  • vitamins
  • K+, Ca2+, Mg2+ (cofactors)
  • trace elements (Fe, Cu, Zn)
46
Q

what do bacterial metabolisms need?

A
  • energy source
  • source of electrons
  • carbon source

bacteria can switch from one metabolism to another depending on the available resources

47
Q

what are the toxic forms of Reactive Oxygen Species (ROS)?

A
  1. superoxide
  2. hydrogen peroxide
  3. hydroxyl radical (most toxic)
48
Q

what is the detoxification reaction in ROS?

A

02 + 4e- + 4H+ = H20

49
Q

what enzymes do bacteria produce to detoxify ROS?

A
  • catalase/peroxidase: convert H2O2 to H20
  • superoxide dismutase + catalase converts O2 to H2O2 then H2O
  • superoxide reductase + catalase coverts O2 to H2O2 then H2O
50
Q

what are the different oxygen requirements for different bacteria?

A
  1. obligate aerobes: catalase + superoxide dismutase
    - use exclusively O2 for respiration
    - P. aeruginosa
  2. facultative aerobes: catalase + superoxide dismutase
    - can use O2 for respiration
    - E. coli
  3. microaerophiles
    - require O2 for respiration
    - C. jejuni
  4. anaerobes aerotolerant: superoxide dismutase
    - do not use O2 for respiration
    - S. mutans
  5. obligate anaerobes = C. difficile
51
Q

what are the 3 direct measurements of bacterial growth?

A
  1. Microscopic counts
  2. flow cytometry
  3. viable counting
52
Q

what are microscopic counts for bacterial growth?

A
  • manually count no. bacteria per unit on glass slide
    ads: cheap
    disads: time-consuming, must be accurate
53
Q

what is flow cytometry?

A
  • machine pumps cell suspension through capillary
  • suspension is hit by a laser and measures scattered light by the bacteria present

ads: can distinguish live/dead bacteria, distinguish specific species using antibodies, high sensitivity
disads: expensive equipment

54
Q

what is viable counting?

A
  • serial dilutions of inoculum is spread on agar
  • colonies are counted using cell counters

ads: distinguishes different species, identifies live bacteria
disads: time consuming, assumes one colony comes from one cell

55
Q

what are the 3 indirect measurements of bacterial growth?

A
  1. optical density
  2. dry weight
  3. metabolic diversity
56
Q

what is optical density?

A

Optical density

  • expose cell suspension to light through prism with given wavelength
  • measure unscattered light, which is proportional to no. cells in suspension

disads: requires high cell densities, doesn’t distinguish live/dead cells, OD values vary depending on organisms, doesn’t work with molds/filamentous bacteria

57
Q

what is the dry weight measurement of bacterial growth?

A
  • measures cell weight after freeze-drying

disads: time-consuming, requires expensive equipment

58
Q

what is the metabolic activity measurement of bacterial growth?

A
  • measure production of specific metabolites
    ads: can measure activity of a specific group of bacteria
    disads: complicated to do
59
Q

what is the bacterial growth curve?

A
  • exponential growth of bacteria

- new generation every 20-30 mins

60
Q

what are the 4 phases of the bacterial growth curve?

A
  1. lag phase
    - metabolism starts, but no division
  2. log phase
    - exponential increase in population
    - logarithmic growth due to binary fission
  3. stationary phase
    - microbial deaths balance production of new cells
    - fermentation releases acidic compounds which lower pH of the medium, so can no longer sustain growth
  4. death phase: decrease in population
61
Q

what is the thermal death point?

A
  • min temp at which all organisms are killed in 10 mins in a particular liquid
62
Q

what is the thermal death time?

A
  • min time required to kill all bacteria in a particular liquid at a give temperature
63
Q

what are the 3 methods microbes can be killed using heat?

A
  1. moist heat (boiling/autoclave): 15 mins at 121C under pressure to kill spores
  2. dry heat (oven): direct flaming, incineration >150C for 2 hrs
  3. pasteurisation (mild heat)
    - HTST: 72C for 15secs, kills 99.9% viable microorganisms in milk
    - UHT: 140C, 2-5secs
64
Q

how can irradiation kill microbes?

A
  • UV, x-rays and gamma rays have short enough wavelengths to kill bacteria
  • the shorter the wavelength, the more energy provided (indirect proportional)

ionising radiations:

  • food industry, medical/lab equip
  • DNA destruction via ROS and breaking double strand

non-ionising radiation:

  • surface decontamination
  • DNA damage
65
Q

how can filtration kill microbes?

A
  • sterilise gases or liquids that can be damaged by heat
  • porosity of filters (1mm to 0.01um) can be chosen for specific microbes
  1. nucleopore filter: membrane with holes that filters microbes
  2. membrane filter: mesh of continuous polymers
  3. depth filters: fibres stuck on top of one another
66
Q

what are bacteriostatic antimicrobial agents?

A
  • doesn’t kill bacteria, only stops growth
  • maintain no. cells
  • maintain viable cell count
67
Q

what are bactericidal antimicrobial agents?

A
  • stop growth

- trigger cell death as viable cell count decreases

68
Q

what are bacteriolytic antimicrobial agents?

A
  • cause cell lysis
69
Q

what are sterilants?

A
  • eliminate all forms of microorganisms, including spores, on objects
  • e.g. ethylene oxide: gas so is effective
  • most powerful antimicrobial compound we can use
70
Q

what are disinfectants?

A
  • kill microorganisms, but not endospores, on objects

- e.g. alcohol (60-85% in water)

71
Q

what are antiseptics and germicides?

A
  • inhibit growth
  • kill microorganisms on tissues
  • e.g. handwash
72
Q

how can antimicrobial activity be measured?

A
  1. disc diffusion technique
  2. Minimum Inhibitory Concentration (MIC): growth inhibition measurement
  3. Minimum Bactericidal Concentration (MBC): cell death measurement
73
Q

what is the disc diffusion technique to measure antimicrobial activity?

A
  1. inoculate plate with a liquid culture sample
  2. discs containing antimicrobial agents are placed on surface
  3. incubate for 24-48hrs
  4. test organism shows susceptibility to some agents, indicated by zones of inhibition
74
Q

what is the MIC growth inhibition measurement of antimicrobial activity?

A
  • MIC is the lowest concentration of a drug inhibiting the visible growth of a test organism after overnight incubation
75
Q

what is the MBC cell death measurement of antimicrobial activity?

A
  • MBC is the lowest conc of a drug killing 99.99% of a test organism after overnight incubation
  • test no. viable cells after being in contact wit antimicrobial agent
76
Q

what are phenolic compounds?

A
  • aromatic derivatives
  • low anaesthetic at low conc, antibacterial at high conc
  • disrupts cytoplasmic membrane and denatures proteins
77
Q

how are alcohols used in antimicrobial control?

A
  • denatures proteins and disrupts cytoplasmic membranes
  • lipid solvent
  • active conc between 60-85%
78
Q

how are aldehydes used in antimicrobial control?

A
  • alkylating agents containing aldehyde groups
  • formalin prevents bacterial growth
  • modify proteins and DNA, leading to cell death
79
Q

what are quaternary ammonium compounds?

A
  • interact with phospholipids of the cytoplasmic membrane
  • cationic detergents
  • long chains with charge tail allows disruption of membrane
80
Q

what are halogen-releasing agents?

A
  1. chlorine-releasing agents
    - bleach ionises to form Na+ and hypochlorite ion OCl-, in equilibrium with hypochlorous acid (HOCl)
    - form chlorinated bases in DNA and oxidation of proteins
  2. iodine-releasing agents
    - iodine/iodophores
    - target DNA and proteins
81
Q

what are the two major therapeutic strategies against pandemics?

A
  1. antibiotics

2. vaccinations

82
Q

who described germ theory?

A

Louis Pasteur 1860

83
Q

what is Koch’s Postulates?

A
  • in 1890s, Koch discovered the causal relationship between a microbe and a disease
  • used germ theory
  1. microbe must be found in all organisms suffering the disease, but not in healthy organisms
  2. microbe can be isolated from diseased organism and grown in culture
  3. cultured microbe should cause disease when applied to healthy organism
  4. microbe is reisolated from the inoculated host and identified as being identical to the original microbe
84
Q

who discovered penicillin?

A

Alexander Fleming in 1928, produced by a fungus mold

85
Q

what are the major classes of antibiotics?

A
  1. Cell wall inhibitors
    - beta-lactams
    - glycopeptides
  2. protein synthesis inhibitors
    - aminoglycosides
    - cyclines
    - MLS
    - oxazolidinones
  3. DNA metabolism inhibitors
    - quinolones
86
Q

what causes antibiotic resistance?

A
  • antibiotic overuse and misuse in human therapeutics
  • farming: animals can be fed with antibiotics at subtherapeutic doses (4x human consumption)
  • agriculture: treatment of diseases in plants
  • aquaculture
  • pets
87
Q

what are the key properties of an ideal antibiotic?

A
  1. It must display selective toxicity towards the target bacteria
    - must inhibit an essential process or inhibit virulence
  2. it must be stable in the host and active at low concentration
  3. It must be cheap
88
Q

what are beta-lactams?

A
  • penicillin antibiotic that inhibits peptidoglycan polymerisation
  • they target D, D-transpeptidase penicillin binding proteins (PBP) in bacteria
  • they form covalent bonds with amino acid in position 4, to form a crosslink from C-terminal to acceptor group
  • they are structural analogs of D-Ala-D-Ala C-terminal residues in peptide stem
  • they are used by PBP as substrates and inactivate these enzymes irreversibly
89
Q

what are the 4 models of antibiotic resistance by bacteria?

A
  1. drug inactivation: beta-lactamases
  2. target modification: low affinity
    PBPs/overexpression
  3. efflux/impermeability: efflux systems in gram -ve bacteria
  4. bypass: alternative pathway
90
Q

what are the 4 methods in which are bacteria resistant to beta-lactams?

A
  1. inactivation by beta-lactamases
  2. mutation of the target enzyme PBP
  3. secretion of the antibiotic by gram negative bacteria
  4. modification of the synthetic pathway targeted by beta-lactams
91
Q

how do bacteria inhibit beta-lactams via beta-lactamases?

A

beta-lactamases can hydrolyse the antibiotic, causing it to become inactive as the structure no longer resembles D-Ala-D-Ala:

  1. nucleophilic attack by catalytic serine
  2. covalent complex penicillin-beta-lactamase
  3. penicillin hydrolysis

beta-lactamases evolved from the same family as PBPs

92
Q

how does mutation in the target enzyme PBP make bacteria resistant to beta-lactams?

A
  • used by gram-positive bacteria

Two methods:
1. They form low affinity PBPs so that there reduced affinity of beta-lactams for PBP

  1. Overexpress PBP targetted by beta-lactams
93
Q

how does mutation in the target enzyme PBP make bacteria resistant to beta-lactams?

A
  • used by gram-positive bacteria

Two methods:
1. They form low affinity PBPs so that there reduced affinity of beta-lactams for PBP

  1. Overexpress PBP targetted by beta-lactams
94
Q

how do gram negative bacteria secrete the beta-lactam in antibiotic resistance?

A

e. g. P. aeruginosa
1. overproduction of the MexAB-OprM system
- carbapenem resistance

  1. Overproduction of the MexEF-OprN system
    - imipenem resistance
95
Q

how do bacteria modify the synthetic pathway that is targeted by beta-lactams in antibiotic resistance?

A
  • they remodel how peptidoglycan is synthesised
  • L, D transpeptidases cause different type of crosslinking which is beta-lactam insensitive
  • they form a 3,3 bond rather than a 3,4 bond

Microbiology (8 decks)

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