Microbiology (core) ->44! not medical Flashcards
Hello its Millie I've finished the questions so it covers all of the lectures fully now!! (158 cards)
1
Q
Who wrote the first book dedicated to microscopic organisms?
A
Robert Hooke
2
Q
Who first described bacteria? What did they refer to them as?
A
- Antoni van Leeuwenhoek
- First described them as animalcules
3
Q
Who disproved the idea of spontaneous generation of microbes? How?
A
- Louis Pasteur
- 2 tubes, where one was briefly expsed to dust and one which was not; only the tube which had touched the dust had its liquid putrefied
4
Q
How were microorganisms discovered? By who?
A
- Careful examination of blood from diseased animals showed presence of bacteria
- Used mice and anthrax (disease caused by a bacterium called Bacillus anthacis) to develop Koch’s postulates
- Robert Koch is the dude
5
Q
What are the 4 Koch’s postulates?
A
- The suspected pathogen must be present in all cases of the disease and absent from healthy animals
- The suspected pathogen must be grown in pure culture
- Cells from a pure culture of the suspected pathogen must cause the disease in a healthy animal.
- The suspected pathogen must be reisolated and shown to be the same as before.
6
Q
What do microorganisms need to be grown in?
A
Culture medium, can be solidified into agar or left as a liquid
7
Q
Why are tubes containing solid agar set in a slope?
A
- Used for pure growth of a microorganisms
- More surface area so can see spread better
8
Q
what is a colony?
A
A single spot of bacteria on a plate
Represents one bacteria that grew and divided
9
Q
What are the 4 types of light microscopy?
A
- Bright field - kills specimen as uses staining
- Phase contrast - doesn’t kill specimen, has a glow around it
- Dark field - doesn’t kill specimen
- Fluorescence - can use dead and living specimen to visualise cells that fluoresce e.g chlorophyl
10
Q
What is differential interface contrast microscopy?
A
A form of light microscopy, which uses polarised light to make structures appear 3D
11
Q
Describe atomic force microscopy
A
Measures forces between a probe and the atoms on the surface of the specimen, measures deviations from the flat surface
12
Q
Describe confocal scanning laser microscopy
A
Couples a laser source to a fluorescent microscope, focuses through the specimen in layers and reconstructs the layers of the specimen to make it 3D, cells are typically dyed with fluorescent stains to make more distinct
13
Q
Describe transmission electron microscopy
A
Uses electrons instead of visible light
Electromagnets function as lenses
uses a vacuum
High magnification
High resolution 0.2nm
Can see molecular level structures
Need thin specimens as electrons don’t penetrate tissues well
Dead sample
14
Q
Describe scanning electron microscopy
A
Uses electrons instead of visible light
Electromagnets function as lenses
uses a vacuum
Shows external surfaces of the cell
Intact specimen is coated with a film of a heavy metal, like gold
Electrons scatter from the metal coating and are collected to form the image
Dead sample
15
Q
Why is it important to understand microorganisms?
A
Agriculture, animal husbandry, fermentation, biofuels, GMOs, gene therapy, disease, food preservation
16
Q
How to generate a phylogenetic tree
A
- Isolate DNA each organism
- Make copies of rRNA gene by PCR
- Sequence DNA
- Analyze sequence
- Generate phylogenetic tree
17
Q
Whats the largest phylum of bacteria?
A
proteobacteria e.g e.coli
18
Q
What are the 2 phyla of archaea?
A
Euryarchaeota and the
Crenarchaeota
19
Q
What are protozoa?
A
Unicellular eukaryotes
* Live in soil, wet sand, fresh
and salt waters
20
Q
What is the cell size range for prokarys and eukaryotes?
A
- Size range for prokaryotes: 0.2um to >700um in diameter
- Size for eukaryotic cells: 10um to > 200um in diameter
- need to be at least 0.15um to fit everything needed in a cell
21
Q
What are endospores?
A
Highly differentiated cells, produced by some bacteria, resistant to harsh environments like heat, chemicals and radiation and used as a survival structure
22
Q
Describe the process of sporulation
A
- An essential nutrient is exhausted
- Vegetative (asexual) cell stops growing
- Endospore develops within vegetative cell and is released
- Spore can remain dormant and then germinate and differentiate into a vegetative cell when conditions are favourable
23
Q
Endospore structure
A
- Strongly refractive and impermeable to most dyes
- Usually seen as unstained regions within cell
- Some made at end (terminal endospores), some made in middle (central endospores), some made in between (subterminal endospores)
24
Q
What structure enables cells to stick to surfaces and each other? Can also assist disease processes
A
Fimbriae - filamentous structures composed of protein extending from surface of cell
25
What structure enables conjugation between cells, mobility, and adhesion of pathogens to host tissues? What microscopy best shows this structure?
- Pili
- Light microscopy
26
Name the 2 kinds of microorganism taxis
Chemotaxis and phototaxis
- attractant causes directed movement otherwise its random movement
- towards attractant = longer runs and fewer tumbles (when flagella are pushed apart)
## Footnote
Taxis is the movement of the micro org towards something beneficial, or away from sopmething harmful (can be chemical or light)
27
Describe flagella structure
Helical
Different wavelength for different species
Filament composed of many flagellin proteins
Can only been seen with light microscope after being stained
28
What are the 3 different types of flagella attachent?
- Polar: on one side of the microbe
- Tuft: a group of flagella attached to one end of the cell
- Peritrichous: inserted at many different locations (and poles of the cell)
29
How do flagella move?
PROTON TURBINE MODEL
- A molecular motor drives rotation (motor: central rod, series of rings, Mot proteins)
- Proton movement across the MOT complex in the membrane gives energy
- Central rod and rings rotate while MOT proteins stay still
- Protons exert electrostatic forces on helically arranged charges on the rings that make up the motor
- Attraction and repulsion causes rotation
| Similar to ATP synthase
## Footnote
Wavelength between curves is characteristic for any given species
30
How do peritrichous flagella change direction?
Bundled flagella move counterclockwise and then tumble (flagella are pushed apart) and move clockwise and then reassemble in other direction to go the other way and move counterclockwise again
31
How do polar flagella change direction?
Reversible flagella change direction from moving counterclockwise to clockwise to move forwards and back
Unidirectional flagella can only go in one direction so rotate clockwise then cell stops and waits until liquid or env moves it and then continues moving flagella in clockwise fashion
32
What are the 2 mechanisms known to be involved with gliding in microorganisms?
1. Polysaccharide slime - slime adheres to surface and pulls cell along
2. Twitching motility - repeated extension and retraction of type IV pili, a bit like rowing and pulling itself along
33
What kind of bacteria can form multicellular structures, and what are these structures?
Myxobacteria
Fruiting bodies (just one example)
Have intercellular communication
34
What is the life cycle of myxobacteria?
Myxspores released when env conditions are favourable
Germination - form gram-negative cells
Vegetative growth cycle
Aggregation
Mounding
Differentiate into fruiting bodies
35
How do myxobacteria move?
They glide - leaving slime behind which is detected by other bacteria so bacteria follows it
36
Autotroph vs heterotroph
- Autotroph: use CO2 as their C source, primary producers, synthesis new organic matter
- Heterotroph: use organic compounds as their C source, either feed directly on other cells or live off products other org.s excrete
37
Where do chemolithotrophs get their energy?
From oxidation of Inorganic chemicals
e.g iron bacteria or sulphur bacteria
- normally waste products of chemoorganotrophs so not in competition
38
What is a chemoorganotroph?
An organism that obtains its energy from the oxidation of organic compounds e.g. glucose, acetate, etc.
39
What is an autotroph?
An organism that makes it own energy from inorganic substances like CO2
40
What energy conversion does any organism that performs photosynthesis use?
Phototrophic
Most are autotrophs
41
What is anoxygenic photosynthesis?
- Don’t split water
- Take sulfur containing compounds to create electrons that way
42
What does a chemolithotroph do?
- Oxidation of inorganic compounds releases energy- stored as ATP
- Only prokaryotes
- Several inorganic compounds can be oxidised, e.g. H2, H2S, NH3
| Imagine the numbers are subscript pls x
43
Define nitrogen fixation
- Converting atmospheric nitrogen gas into a form usable by cells
- N2 --> NH3
- no known eukaryote can fix nitrogen
## Footnote
There is a longer equation, but just remeber N2 --> NH3
44
2 types of nitrogen fixing bacteria
1. Free-living
2. Symbiotic - e.g in root nodules
45
What enzyme catalyses nitrogen fixation?
Nitrogenase
46
What is nitrogenase composed of?
Dinitrogenase - contains iron and molybdenum
Dinitrogenase reductase - contains iron
47
What reaction does nitrogenase catalyse?
Converting nitrogen into ammonia:
N₂ + 8H⁺ + 8e⁻ → 2NH₃ + H₂
48
What is the second step in the nitrogen cycle?
Nitrification
49
Describe nitrification
- Oxidation of ammonium into nitrites NO2-, and then into nitrates NO3- by **nitrifying bacteria**
- NH4+ --> NO2- --> NO3-
50
What are the 2 kinds of nitrifying bacteria? Where are they found?
- Nitrosomonas and nitrobacter
- They are widely distributed in soils and H2O
51
What reaction do nitrosomonas and nitrobacter each perform?
- Nitrosomonas: NH4+ --> NO2-
- Nitrobacter: NO2- --> NO3-
## Footnote
There are wider reactions but this is the important part, and energy is produced in both of these reactions
52
Why is N2 fixation and nitrification important for sewage and water treatment?
To remove toxic amines and ammonia
53
What is denitrification?
The conversion of nitrates (NO₃⁻) back into nitrogen gas (N₂) by denitrifying bacteria, releasing it into the atmosphere.
54
What is humus?
Complex mixture of organic materials
that have resisted rapid decomposition,
derived primarily from plants and
microorganisms
- most carbon is found here
55
What is the most important contributor of CO2 to the atmosphere?
**Microbial decomposition** of dead organic material and humus
56
What is growth in single celled organisms compared to multicellular organisms?
Single- celled organisms - Growth is defined as an increased number of cells in a population
Multicellular organisms: - Growth involves
the whole organism getting bigger
57
How do prokaryotes grow/divide?
Binary fission
One cell divides into 2
58
What is generation time?
- Time required for binary fission to occur and produce 2x daughter cells
- how long it takes for population to double in size
- varies in species and also on nutritional and environmental factors
- n = logN (final cell number) - logN0 (initial cell number) / 0.301
- or g = t/n which is time / number of generations during exponential growth
59
Give the basic steps of binary fission
1. Cell replicates DNA
2. Cytoplasmic membrane elongates
3. Cross wall septum forms
4. 1 parent cells forms 2 daughter cells
60
Define bacterial growth
The increase of cells within a population
61
How do we refer to exponential growth between generations?
- We work in base 2
- e.g. generation 0 (1 cell) = 2^0, generation 1 (2 cells) = 2^1
## Footnote
N = N0 x 2^n5r
62
why might be length of the lag phase be longer?
When moving from a old culture with damaged cells into a fresh culture woith good growth conditions it can take the bacteria some time to reach the exponential phase
## Footnote
Bacteria from cultures with optimal growth conditions have a shorter lag period when transferred - almost no lag phase even
63
What is the healthiest cell state of the bacterial growth curve?
The exponential phase
64
What are the 3 ways of measuring bacterial growth?
1. Microscopic counts - counting chamber or flow cytometer or bacteria dried on slides
2. Viable counts - plate count (spread plate and serial dilution or streak plates)
3. Spectrophotometry - more light scattering = more cell mass (turbidity) = more cells
65
what is the main assumption with viable counts?
1 viable cell = 1 colony
66
What are the main sources of error in a viable/plate count?
- Culture medium, incubation conditions and time have a big effect and need to be closely controlled
- Not all cells grow at the same rate (in mixed cultures)
- May miss small colony sizes
- Inaccurate pipetting, non-uniform sample, insufficient mixing, heat intolerance, etc
67
What is the main concept behind spectrophotometry as a method to count bacteria?
- cells scatter light
- Turbidity can therefore be used to estimate cell mass in a sample
- more light scattering = more cell mass = more cells
68
issues with spectrophotometry
- Turbidity doesn't equal number of cells
- Debris causes falses positive
- Cell clumping messes with reading
- Diff wavelengths also give diff density measurements
- Can only be used with clear broths
69
How do you measure oxygen concentration in a soil particle? What distribution of O2 would you expect across the particle?
Microelectrodes
- Would see a normal level of oxygen at top/surface
- In depth/ centre of particle, theres no oxygen (bc microbes around particle are using oxygen in respiration and rate of diffusion is slower than rate of uptake from microbes; it can't be saturated with oxygen as its taken up before it can reach the middle)
- Anaerobic organisms therefore thrive at the centre
- Anaerobic organisms thrive at the outer layers of soil particles
70
Where does the most extensive microbial growth take place in soil?
On the surfaces of soil particles
71
What is the rhizosphere? What does it provide nutrients?
- Soil near plant roots
- Roots exude lots of nutrients that thee microbes can absorb
72
What effect does water content of soil have on its oxygen levels?
Waterlogged soil = low O2
73
What is groundwater?
Water in soils and rocks **deep underground**
74
How far down into the earth does microbial life extend to?
At least 3 Km
## Footnote
Chemolithic and autotrophic bacteria and archea found in South Africa
75
What does benthic mean?
## Footnote
This is a category of freshwater oxygenic phototrophs
Attached to the bottom or sides of the lake or stream
76
What does planktonic mean?
Floating
77
Which tends to have higher microbe concentrations: freshwater or marine?
Freshwater
78
What are typical characteristics of microbes living in the ocean?
- Very small cells - require less energy for maintenance
- Have a greater number of transport enzymes to acquire nutrients from the dilute environment
## Footnote
Dilute in terms of nutrients
79
What are the more productive regions of the ocean?
Coastal areas - shallower more O2 and light penetration
## Footnote
Ocean microbes contribute hugely to carbon cycling bcs the ocean are so vast
80
What is the photic zone?
- Where light can penetrate to
- Bacteria predominate in water above 1000m
81
Where contains the largest microbial biomass on earth?
The oceans
82
List 7 abiotic growth factors
Light
pH
Temperature
Oxygen
Pressure
Moisture
Nutrient availability
83
What are the 3 most important abiotic growth factors?
1. Temp
2. pH
3. Oxygen
## Footnote
Temperature is argued to be the most important factor affectign microbial growth
84
What are the minimum, maximum, and optimal temperatures called?
**The cardinal temperatures**
- minimum temp – growth not possible below, membrane gelling, growth cannot occur
- optimum temp – growth is most rapid
- maximum temp – growth isn’t possible above, enzymes denature, temp crisis point
**vary in each species**
85
What are the names given to the different ranges of cardinal temperature tolerances?
- Cold: psychrophile
- Medium: mesophile ~40 degrees
- Hot: thermophile
- V hot: hyperthermophile
86
What is the pH growth range for microbes normally?
2-3 pH units
87
What is the most common natural environment pH range?
pH between 4 and 9
## Footnote
Organisms adapted to this range are the most common
88
What must internal, or intracellular, pH remain?
Intracellular pH must remain relatively close to neutrality
89
What does facultative aerobe mean?
Under appropriate nutrient conditions will grow under
either oxic or anoxic conditions
## Footnote
They tend to prefer anaerobic conditions
90
What does microaerophilic mean?
They can onyl use O2 when its at low levels - lower than the air
91
What does aerotolerant mean?
- Anaerobic but can tolerate oxygen
However, they do not use oxygen in their
metabolism
- Unlike anaerobic which may be killed by oxygen present
## Footnote
They dgaf about O2 theyre sooo tolerant
92
Define extremophile
An organism whose growth is DEPENDENT on
extremes of temperature, salinity, pH, pressure, or radiation, which are generally inhospitable to most forms of life
93
What is a halophile?
Requires NaCl for growth
94
Define halotolerant
Can tolerate NaCl, but grows best in absence of a solute
95
Define psychrophile
Grows at 15 degrees and low
Grow at extremely low temperatures
Killed by warming
96
Define psychrotolerant
- Can grow at zero degrees but optimum is 20-40 degrees
- Found more in temperate climates
## Footnote
Therefore more widely tolerated
97
Molecular adaptations to the cold of enzymes
- Have lower optimal temperatures
- Primary structure: more polar amino acids in primary structure
- Secondary structure: more alpha helices for flexibility in
98
What are the adaptations of cytoplasmic membranes to the cold?
- Higher conc. of unsaturated and shorter-chain fatty acids
- This helps the membrane remain semifluid despite low temps
99
What are cold shock proteins?
Maintain other proteins activity and bind specific mRNAs to facilitare their translation
## Footnote
This is not limited to psychrophiles btw!!
100
What are cryoprotectants?
Solutes (e.g glycerol or sugars) that help prevent the formation of ice-crystals in the cell
101
What is a thermophile?
- Growth temperature optimum greater than 45 degrees
- Less extreme than the hyperthermophiles (opt temp is over 80 degrees) - only prokaryotes,
## Footnote
Found in a wide range of warm envrionments
102
What are the most thermophilic prokaryotes?
Archaea
103
Can phototrophic or non-phototrophic organisms tolerate higher temperatures?
Non-phototrophic
104
Molecular adaptations to enzymes and proteins for high temperatures
- Similar amino acid sequences to heat-sensitive forms but with critical amino acid substitutions at a few locations to allow the protein to fold in a heat stable way
- More ionic bonds between basic/acidic amino acids
- Often highly hydrophobic interiors
- All make a protein more resistant to unfolding
105
Molecular adaptations to DNA for high temperatures
- Increased cellular compatible solute levels - prevents chemical damage to DNA
- Reverse DNA gyrase introduces positive supercoils into the DNA which make it more heat-stable
## Footnote
Commpatible solutes are small molecules that the DNA can turn into that can provide additional protection whilst still maintaining function
106
What are the adaptations of heat stable cell membranes that allow them to survive high temps?
- More saturated fatty acids (membrane becomes less fluid)
- More long-chain fatty acids (have a higher melting point)
107
What are the adaptations of **hyperthermophile** cell membranes that allow them to survive high temps?
- Don't have fatty acids
- Have **C40** hydrocarbons (repeating **isoprene** units) bonded to glycerol phosphate by **ether linkage** (rather than ester)
- Form a monolayer
## Footnote
Mainly archaea
108
What are acidophiles?
- Grow best at pH 5.5 or below
- Those with a pH optima of below 1 are very rare
- Most can’t grow at pH 7
109
What are alkaliphiles?
- Grow best at Ph 8 or above
- A few extremophiles have a v high pH optima – as high as pH 11
- Found in soda lakes and high-carbonate soils
- Use sodium instead of protons
110
What must cytoplasmic pH remain near?
Neutral
- Optimal pH for growth refers to extracellular env only
- Intracellular pH must stay near pH 7 to prevent destruction of macromolecules
111
What are compatible solutes?
Organic compounds that are highly soluble, neutrally charged, and dont interfere with cellular metabolism
e.g. proline, glycine betaine, sucrose, trehalose, glycerol
112
What was Waksman's original (1930) definition of an antibiotic?
A compound produced by a microbe to destroy other microbes.
113
What is an antimicrobial?
A compound that kills or inhibits microbes, including bacteria, fungi, and viruses.
114
What is the modern definition of an antibiotic?
A chemical compound with a single mode of action, effective only against bacteria.
115
Who discovered penicillin and when?
Alexander Fleming in 1928.
116
How did antibiotics impact mortality?
Significantly reduced deaths from infections, including childbirth-related deaths.
117
What does a bacteriostatic antibiotic do?
Inhibits bacterial growth without killing the bacteria.
118
What does a bactericidal antibiotic do?
Kills bacteria without lysing them; reduces viable cell count.
119
What does a bacteriolytic antibiotic do?
Kills bacteria by lysing the cell membrane; reduces total and viable cell count.
120
What are the advantages of narrow-spectrum antibiotics?
Target specific bacteria, lower resistance risk, less microbiome disruption.
121
What are the disadvantages of narrow-spectrum antibiotics?
Require accurate and fast diagnosis.
122
What are the advantages of broad-spectrum antibiotics?
Can be used before identifying the pathogen.
123
What are the disadvantages of broad-spectrum antibiotics?
Higher resistance risk and disruption of normal microbiota.
124
What is the mode of action of β-lactams?
Inhibit bacterial cell wall synthesis (bactericidal).
125
Give examples of β-lactam antibiotics.
Ampicillin, Cephazolin, Imipenem.
126
What are common side effects of β-lactams?
Allergic reactions.
127
What do sulfonamides target?
Dihydropteroate synthase (blocks folate synthesis, bacteriostatic).
128
Example of a sulfonamide drug?
Sulfamethoxazole (with Trimethoprim).
129
Common side effects of sulfonamides?
Hypersensitivity, insomnia, blood disorders.
130
How do fluoroquinolones work?
Inhibit DNA gyrase/topoisomerase IV (bactericidal).
131
Give examples of fluoroquinolones.
Ciprofloxacin, Norfloxacin, Moxifloxacin.
132
Side effects of fluoroquinolones?
Tendon damage, blood sugar fluctuations.
133
What is the action of macrolides?
Inhibit protein synthesis (bind 50S subunit, bacteriostatic).
134
Give examples of macrolides.
Azithromycin, Clarithromycin, Erythromycin.
135
Common side effects of macrolides?
Arrhythmias, liver toxicity.
136
What is the mode of action for tetracyclines?
Inhibit protein synthesis (bind 30S subunit, bacteriostatic).
137
Examples of tetracyclines?
Doxycycline, Minocycline, Tetracycline.
138
Side effects of tetracyclines?
Tooth discoloration, photosensitivity, liver toxicity.
139
How do aminoglycosides work?
Inhibit protein synthesis (bind 30S, bactericidal).
140
Give examples of aminoglycosides.
Streptomycin, Gentamicin, Neomycin.
141
Side effects of aminoglycosides?
Kidney toxicity, hearing loss, neuromuscular blockade.
142
Why can’t antibiotics treat viral infections?
They only act on bacteria.
143
When might antibiotics still be used during a viral infection?
To treat secondary bacterial infections.
144
What factors affect antibiotic dosage?
Age, weight, liver/kidney function, infection severity.
145
Why might IV antibiotics be used instead of oral?
Some antibiotics aren’t absorbed well orally.
146
Why should treatment duration be carefully managed?
Too short = ineffective, too long = resistance/side effects.
147
What % of antibiotics are used in livestock?
0.64
148
Why are antibiotics used in agriculture?
Disease prevention, growth promotion, feed efficiency.
149
What is the consequence of agricultural antibiotic use?
Increased antibiotic resistance.
150
What contributes to antibiotic misuse?
Overuse, incomplete courses, poor diagnostics, hospital hygiene.
151
Why has Big Pharma reduced antibiotic development?
High R&D cost ($1.5B), low returns ($46M/year), restricted use.
152
What is the 'post-antibiotic era'?
A time when antibiotics may no longer be effective due to resistance.
153
Name 3 WHO priority resistant bacteria.
Acinetobacter baumannii, Pseudomonas aeruginosa, E. coli.
154
How are new antibiotics being discovered?
Genome sequencing, resistance gene screening.
155
What are AMPs (antimicrobial peptides)?
Natural defense peptides, broad-spectrum, but toxic to humans.
156
What is an example of an anti-virulence drug?
Sibofimloc (blocks E. coli adhesion).
157
What are combination therapies in antibiotics?
β-lactams + β-lactamase inhibitors.
158
What is bacteriophage therapy?
Viruses targeting specific bacteria; requires personalized matching.
