Microbio 1/2 Flashcards
1
Q
What is miasma theory?
A
- stated diseases (cholera, plague) were caused by “bad air” or “night air”
- prevailing theory until 19th century
- no recognition of microbes
2
Q
What was the purpose of the “beak” of the plague mask?
A
- herbs (ex: lavender) in the beak to make the air smell good (eliminates bad air), obviously useless
3
Q
Who was Robert Hooke (1635-1703)?
A
- built the first compound lens microscope (30x magnification)
- first to “see” and record eukaryotic microbes
- coined “cell” from Latin cella meaning small room, after observing cork tissue (small cells with borders)
- provided and wrote of the first images of microbes via magnifying glass, very controversial and not very accepted (challenged what people thought)
4
Q
Who was Antonie van Leeuwenhoek (1632-1723)?
A
- worked in cloth quality, investigating thread count via magnifying lenses with up to 500x magnification
- mounted single lenses on sample holder and focus adjustment
- first to observe single-celled organisms (“animalcules”)
- drew what he discovered
- Leeuwenhoek microscope
5
Q
What can the naked eye see?
A
up to 200nm
- microbes are around 5nm
6
Q
What is the spontaneous generation theory?
A
- theory that living creatures could arise from non-living matter
- microbes came from nowhere- came from how meat sat out would attract maggots over time
- by late 1600s/early 1700s there is evidence to disprove this, though not widely accepted
- Still no evidence links microbes to infectious diseases
7
Q
What did Lazzaro Spallanzani (1760s) prove?
A
- first to show that meat broth sterilized by boiling & not exposed to air failed to grow a ‘life source’
8
Q
How has life expectancy changed from 1770-2021
A
- infectious disease has been the leading cause of mortality worldwide
- low life expectancy in 18th century- 40 years old was good, 60/70 exceptional
- increased mid 1850s drastically
9
Q
What is the bubonic plague?
A
- caused by bacterium YERSINIA PESTIS
- recurring from 6-17th century
- spread by fleas and rodents, related to poor
sanitation, causes infection of the lymph nodes - major European epidemic 1345-1355
- no recognition for necessary sanitization or that it came from rats, did not know what microbes were
10
Q
What was the black death?
A
- 100-200 mil deaths in Europe from the bubonic plague (45-50% European population died in 4 years)
- for reference: covid has killed 7 million as tracked in april 2024
11
Q
What is smallpox?
A
- caused by VARIOLA VIRUS
- Causes small skin lesions, highly contagious, airborne
- Evidence of smallpox from Egyptian mummies (~3000 years ago)
- Leading cause of death in 18th century Europe, ~400,000 people died from the disease per year
- Infects multiple organs, ~30% mortality
12
Q
How did small pox affect the Indigenous?
A
- believed responsible for death of ~90-95% of Indigenous people after European contact; decimated native American communities (no immunity)
- when Europeans colonized America, the Indigenous did not develop immunity from it like the Europeans had at the time
13
Q
What is cholera?
A
- caused by bacterium VIBRO CHOLERAE
- Causes infection of small intestine, severe
diarrhea, vomiting and dehydration - Transmission through contaminated food
and water (they were unaware of why this was dangerous exactly) - Major worldwide epidemics throughout 19th and early 20th Century, ~50 million deaths over first 3 epidemics
14
Q
What is the germ theory?
A
some diseases are caused by microorganisms
- Solidify Germ Theory and promoted the ideas of sanitation and hygiene by end 19th century
- Gained widespread acceptance in 19th Century; contributors: Florence Nightingale, Louis Pasteur, Joseph Lister
15
Q
Who was Florence Nightingdale?
A
British nurse: founder of professional nursing
- founder of modern stats
- 1855; tracked causes of deaths during Crimean war
- found more soldiers died of microbial infections than of battle wounds
- Shows statistical correlation of sanitation with mortality
- Convinced British government to improve living conditions for soldiers
16
Q
Who was Louis Pasteur?
A
- french chemist + microbiologisst
- Major contributor to medical microbiology and immunology
- discovered microbial fermentation produces lactic acid or alcohol (1857)
- showed microbes fail to appear spontaneously using swan-necked flasks (1864) (major evidence for germ theory)
- Development of first artificial vaccine (against anthrax; 1881)
- Developed pasteurization techniques for milk
17
Q
Who was Robert Koch (1843-1910)?
A
- german physician: Founder of the scientific method of microbiology
- Developed Koch’s Postulates (still in use today!), First to use an animal model system, Developed the pure-culture technique
- Used these techniques to prove that tuberculosis (TB) is caused by Mycobacterium tuberculosis; Nobel prize in 1905
- discovers the specific agents (bacteria) responsible for TB, anthrax, and cholera
18
Q
What is the pure-culture technique?
A
pure-culture: only one strain or clone is present
1. microbe found in all cases of the disease
2. microbe isolated from the diseased host and grown in pure-culture
3. when the microbe is introduced into a healthy susceptible host, the same disease occurs
4. the same strain of microbe is obtained from the newly diseased host
19
Q
Who were some important contributors to Koch’s work?
A
Julius Petri: discovered and developed the culture plate (dish) used to this day (Petri Dish/Petri plate)
Angelina & Walther Hess: First to develop solid medium to culture bacteria (can pour solid medium into petri dishes and isolate bacteria)
20
Q
Who was Joseph Lister?
A
- a surgeon who realized gangrene and death after surgery was due to infection
- pioneer antiseptic practice during surgery, using carbolic acid (phenol) spray to sterilize surgical instruments, clean wounds (pure phenol denatured protein and burned skin)
- made surgeons wash hands in diluted phenol and wear gloves
21
Q
Who was Edward Jenner?
A
- finds milkmaids exposed to cowpox are immune to the more severe smallpox
- Tests this by inoculating a child with pus from cowpox blisters (he did not develop smallpox), develops the first smallpox vaccine (ethics??)
- first person to provide scientific evidence for the deliberate use of vaccination to control an infectious disease
22
Q
Who was Carl Woese?
A
- studied bacteria that have adapted to life in extreme environmental conditions
- analyzed 16S ribosomal RNA (rRNA) gene sequences and revealed that these prokaryotes were a distinct life form
- coined the name Archaea (Greek for “ancient things/cells”)
23
Q
What are archaea?
A
- prokaryotic but not bacteria
- found in extreme environments
- completely unrelated to the other two domains of life (bacteria and eukarya)
24
Q
Why are viruses not considered a domain of life?
A
- they are not living entities: they need a host to replication, by itself it would die off
- they are wayyy smaller than bacteria (in nanometer range)
- uncommon for viruses to jump between organisms
EX: Covid, smallpox
25
Who was Dmitri Ivanovsky?
- discovered a disease-causing agent so small that it passed though 0.1 μm pores in a filter
26
Who was Martinus Beijerinck?
proposed the filtrable agent was not a bacterium; it was a novel unknown microbe coined ‘virus’ (latin for poison) (because they infect something)
27
Who was Wendell Stanley?
later purified & crystallized the agent & using electron microscopy identified the Tobacco Mosaic Virus (TMV)
28
Why was the "Spanish Flu" an inaccurate name for the influenza pandemic during WW1?
Spain did not contribute to world w1, they reported the deaths but did not start the flu
29
How did WW1 speed up the pandemic's progress?
crowded clinics, trenches, global population movement, malnourishment
- exaggerated the impact
- Infected 500 million people worldwide, 50-100 million died (3-5% world population)
- no vaccination
30
Who was Sir Alexander Fleming?
- scottish medical researcher living in britain
- finds mould Penicillium notam inhibits growth of Staphylococcus bacteria, isolates “penicillin”
-
31
Who was Mary Hunt?
- accomplice of Fleming
- found more efficient penicillin-producing Penicillium rubens strain on a cantaloupe
- made more penicillin than what fleming originally found, so used in large amounts (for manufacturing, originally by Pfizer)
- synthetic antibiotics later developped
32
How did life expectancy increase?
- increased sanitation and hygiene
- later: discovery of antimicrobial drugs and vaccines
33
What are a concern about global and infection + diseases?
- Emergence & re-emergence of infectious diseases (HIV/AIDS; Ebola; COVID19)
-> Changing susceptibilities
-> Infections in patients with compromised immune systems (from HIV/AIDS, cancer, chemotherapy, immunosuppressant drugs, organ transplants, aging)
-> Disruptions of microbiome (prolonged antibiotic treatments; stress; malnourishment; etc.)
34
What is another concern about global and infection + diseases?
- Population density & Globalization
-> earth growing at a tremendous state
-> growing population density can spread diseases faster
35
What is a third concern about global and infection + diseases?
- Climate change / global warming
-> microbes don’t grow in colder environments: if temp rises, all inhibited microbes would grow in warmer environment, especially if humid
-> fungal diseases especially are worrisome: the region in which they can grow expands
-> plants also susceptible to fungi: food resources also would decrease
36
What is the AMR crisis? (Antimicrobial drug resistance)
- increase in antibiotic use creating drug resistance increase (microbes mutate to survive)
- 2 million cases of drug resistant infections in the US/year
- >5 million global human deaths were associated with AMR among bacterial pathogens in 2019
- Each year in Canada, AMR is responsible for ~$2 billion in medical care costs
- Escherichia coli and Staphylococcus
aureus were the leading pathogens
associated with resistance in 2019
37
Do all microbes cause disease?
- no, most do not and they are essential to all aspects of life on the biosphere
- arose with the development of new technologies
38
How is human health affected by infection and diseases?
- impact of microbiome on human health largely uncharacterized
- Evidence linking composition and function of gut microbiome to diseases
- Enormous microbial diversity; poorly characterized and not well understood
39
What is fermentation?
occurs in absence of oxygen, microbe thrives as they want energy to grow
39
Why do people eat kombucha and kimchi?
- to sustain health of the gut microbiome, makes metabolize
40
How are prokaryotes different from eukaryotes?
- no membrane-bound organelles (nucleus)- they have nucleoid
- unicellular
- smaller in size
- not found in tissue
- divide through binary fission (eukaryotes divide through mitosis/meiosis)
41
What is the cell wall made of in bacteria, fungi, and plants?
bacteria = peptidoglycan
fungi = chitin (deadly to humans)
plants = cellulose
42
What does phototrophic mean?
can synthesize (make their own energy from sunlight)
- bacteria, plant, algae
43
What does heterotrophic mean and what are some examples?
- they get energy from simple sugars (do not synthesize their own)
bacteria + fungi + mammals + protists
44
What does phylogenetic mean?
- Evolutionary development (descent) and diversification of organisms from a common ancestor
- divergencies
45
What is the endosymbiont theory?
- explains origin of eukaryotic cells from prokaryotic organisms
46
What did mitochondria and chloroplasts descend from?
- free-living prokaryotes that started living inside pre-eukaryotic cell in endosymbiosis
- Mitochondria: respiring proteobacterium; generated heterotrophic eukaryotes (critical for survival)
- Chloroplasts: photosynthesizing cyanobacterium; produced phototrophic eukaryotes
47
What are 4 non-beverage fermented food products?
- yogurt
- pickles
- tofu
- bread
etc
47
What are 4 concerns regarding infection and diseases?
- global warming/climate change
- population density + globalization
- changing susceptibilities of diseases
- antimicrobial resistance
48
Who was Carolus Linnaeus (1701-1778)
- father of (Linnaean) taxonomy
- invented the system for naming and classifying organisms; binomial nomenclature
- assigned organisms into genus' and species: through different characteristics
- 3 kingdoms: animal, plant, mineral (later abandoned)
49
What is the taxonomic hierarchy of classification?
- hierarchy of groups of related organisms (taxa) based on successively narrow criteria
- now based on DNA sequence similarity
49
What is the sequence of taxons
domain > division (phylum) > class > subclass > order > family > genus > species
50
How can we define a species?
- high degree of genomic relatedness based on housekeeping genes;
orthologs
-> Small SubUnit (SSU) rRNA genes (16S rRNA for prokaryotes): 95% identity = same Genus
S: Svedberg units; relates sedimentation coefficients
- Shared common traits and ecological niche (ecotype)
-> Shared traits like cell shape, nutrient requirements, habitat (can be variations within species)
51
How do we write species names?
- write genus and species
- genus is always capitalized, species is never
- written in italics
52
Describe bacteria
- in nearly every habitat on earth
- most harmless/beneficial (small pathogen number)
- most cell walls containing peptidoglycan (polymer with sugars and amino acids
- photosynthetic (cyanobacteria) or non-photosynthetic
- enormous metabolic diversity
- large size differences
53
What are some bacteria examples?
- coccus (cocci): small spheres (200um)
- bacillus (bacilli): pill-like
- vibrio: rounded eyebrow
- coccobacillus: mix of cocci and bacilli size (2 um)
- spirillum: spiral
- spirochete: corkscrew (500 um)
54
Describe archaea
- found in nearly every earth habitat
- extremophiles (live in niches where you'd think organisms could not live)
- vastly different from bacteira
- cell walls have pseudopeptidoglycan (different in genetics, metabolic pathways, membrane compositions; some components of peptidoglycan)
- archaea have vastly different cell walls depending on conditions
55
Give some examples of archaea (the conditions they live in and real-life implications)
- hot springs (up to 100C)- thermophiles
-> they make DNA at warm temperature
-> DNA polymerase functions at 80C: can use their DNA polymerase to do DNA synthesis at high temp
- living at below 0
-> have lipases: break down fat at cold temps
-> lipase in laundry soap: breaks down stains in cold temps.
- high salt conc.
56
What are domain eukarya? (4)
- protists
- fungi
- plants
- animals
- eukaryotic cell structure, defined nucleus
- typically larger than bacteria
57
What are protists?
- anything except plants, animals, or fungi
- so many; cannot efficiently categorize them
- can live as single cells or in larger multicellular communities
58
What is algae?
- broad characteristic of protists
- unicellular or multicellular and vary widely in size, appearance, and habitat
- cell walls: cellulose
- photosynthetic !!
59
What is protozoa?
- broad characteristic of protists
- very diverse
- move with cilia/flagella
- some photosynthetic, parasitic, pathogenic
ex: paramecium
60
What are fungi?
- Unicellular or multicellular
- Non-photosynthetic
- cell walls: chitin
- heterotrophic: cannot make their own energy (take it up from environment)
- secrete enzymes that break down extracellular cellulose
- biggest organisms on planet
61
What are yeasts?
- unicellular
- Large impacts in food production & safety
- Can cause gonadal infections and oral thrush
62
What are Molds / filamentous fungi?
- multicellular
- made of long filaments that form visible colonies
- play acritical role in decomposition and nutrient cycling (saprotrophs)
- used to make pharmaceuticals (penicillin, cyclosporine)
- darker: oldest part of colony
63
What are viruses?
- acellular microorganisms with proteins and genetic material (DNA or RNA) inert outside of a host organism
- hijack the host’s cellular mechanisms to multiply and infect other hosts
- can infect all types of cells
- responsible for numerous diseases in humans
64
What is a petri dish?
flat-lidded dish that is typically 10–11 centimeters (cm) in diameter and 1–1.5 cm high
65
What are test tubes?
sterile, capped cylindrical plastic or glass tubes with rounded bottoms
- sterilized by autoclaving
66
What is a bunsen burner?
- metal apparatus that creates a flame burning gas
- used to sterilize pieces of equipment
67
What is an inoculation loop?
- handheld tool that ends in a
small wire loop
- used to streak microorganisms on solid medium in a Petri dish or to transfer them from one test tube to another
68
What happens if we do not sterilize the inoculation loop?
whatever growing in lab would stick to it and affect the plate
- sterilized when put into bunsen burner (working aseptically)
69
What are microscopes?
- produce magnified images of microorganisms, human cells and tissues
70
What are stains and dyes?
- add colour to microbes so they can be better observed
- fixation may be required
- cellular chemical composition
- dye bonds to structure and cells
71
What is growth media?
- used to grow microorganisms in a lab setting
- Liquids and/or solid
- provides nutrients, including water, various salts, a source of carbon (like glucose), and a source of nitrogen and amino acids (like yeast extract)
- microorganisms can grow and reproduce
- some microorganisms we do not understand enough to culture (grow)
- must match microorganisms to grow to their required nutrients
72
What can we see with a light microscope?
- generally: bacteria, archaea, yeasts
73
What is light, generally?
- match microorganisms to grow to their required nutrients
- wavelength (lambda) increases, energy decreases
74
What does resolution require?
- contrast: Able to distinguish object from its surroundings
- Wavelength: needs to be equal to or smaller than the object to be resolved
- Magnification: Human retina absorbs radiation in 380-750 nm range
75
How does light interact with an object?
absorption, reflection, refraction, scattering
76
Describe light microscopy
resolves images according to absorption of light
77
Describe electron microscopy
uses beams of electrons to resolve smaller details (smaller than the wavelength of visible light)
78
Describe atomic force microscopy
uses intermolecular forces to map 3D- topography of the cell
79
Describe X-ray crystallography
detects the interference patterns of X-rays entering the crystal lattice of a molecule
80
What are the 4 types of light microscopy?
- Bright field microscopy
- Dark field microscopy
- Phase-contrast microscopy
- Fluorescence microscopy
81
Describe resolution
- the ability to distinguish between two separate points.
- Human eye can resolve two points ~150 μm apart.
- A low-resolution image appears fuzzy, whereas a high- resolution image appears sharp. Affected by wavelength and numerical aperture.
82
Describe contrast
- difficult to distinguish small structures in microorganisms due to transparency
- mechanisms to increase contrast to resolve detect different structures
83
Describe magnification
- the ability of a lens to enlarge the image of an object when compared to the real object
84
What is the numerical Aperture (NA)?
higher the NA, the higher the resolving power of the objective
85
What is a compound microscope for light microscopy?
Has a system of multiple lenses designed to focus, correct and/or compensate for aberration of the objective
- has ocular lenses and objective lenses
86
List the features named on lenses
magnification (x10..), numerical aperture (/1.25), immersion objective (oil)
87
How can we find the total magnification?
__X ocular lens & __X objective
10x x 100x
= 1000x
88
Describe oil immersion and why we choose it
- drop of oil between lens and object
- minimum loss of refracted light at widest angles and sharpens image (increases light view- same refractive index as glass, light would travel straight)
- only specific oils
89
What are the advantages and disadvantages of bright field microscopy and staining?
AD: observation of cells in natural state
DIS: little contrast between transparent cell and background (detection and resolution of cells under microscope enhanced by staining)
90
What is bright field microscopy?
- most common type of light microscopy
- object appears as dark silhouette, blocking passage of light
- resolution limit is approx 1000x
91
What is a wet mount and how do we properly apply it?
- a drop of water on a glass slide with a coverslip
- start on angle and then slowly drop slide so no air bubbles
92
What is the difference between a simple and differential stain?
simple: adds dark color specifically to cells, but not external medium or surrounding tissue (methylene blue)
differential: stains one kind of cell but not another (gram stain)
*know methods of gram stain and methylene blue !
93
What is gram-positive bacteria?
- retain the crystal violet stain because of thicker cell wall, cells appear purple
94
What is gram-negative bacteria?
- bacteria do not retain the stain, cells appear a pinkish/reddish colour
- thin cell wall
95
What is acid-fast staining?
- differentiate two types of gram-positive cells (those with waxy mycolic acids in cell walls and those that do not)
*know method !
96
What is capsule staining?
- capsule: protective outer structure called capsule
- presence of capsule directly related to microbe's virulence (ability to determine whether cells in a sample have capsules is important tool)
- negative staining technique required (india ink stains surrounding medium, not capsule: translucent, looks white under microscope)
97
What is endospore staining?
endospores: structures produced within certain bacterial cells that allow them to survive harsh conditions
- bacillus species form highly resistant endospores (resistant to normal staining)
- endospore stains green
98
What are the 4 different types of staining?
endospore, capsule (negative), acid-fast, gram
+ simple with methylene blue
* know each method
98
What is phase contrast microscopy?
- exploits differences in refractive index between the cytoplasm and the surrounding medium or between different organelles
- Contrast between cells and background is increased
- reveals differences in refractive index as patterns of light and dark
- can be used to view live unfixed cells and cellular organelles
99
What is fluorescence microscopy?
- tool for detecting parts of cells
- specimen absorbs light of defined wavelength, emits light of lower energy (longer wavelength), specimen fluoresces
100
What is autofluorescence in fluorescence microscopy?
- some cell components naturally fluoresce under specific light wavelengths; no stain required
101
What are fluorophores in fluorescence microscopy?
- fluorescent compounds (e.g., FM4-64; DAPI) or proteins (e.g., GFP, YFP, CFP, etc.) that can fluoresce
- they bind to proteins, allowing us to tag and follow location of proteins (Pol-YFP, Ori-CFP)
- specificity determined by: chemical affinity, labelled antibody, DNA hybridization, gene fusion reporter tags (i.e., GFP)
102
What is immunofluorescence?
- technique that identifies certain disease-causing microbes by observing whether antibodies bind to them
(1- antigen fixed to surface, 2- patient serum added: present antibodies bind to antigen, 2- 2nd antibody with fluorescent label added: if patient antibodies present, they bind)
103
How is an electron microscope better than light microscopy?
- much higher energy than light, increases resolution
- uses beams of electrons instead of light in visible spectrum for visualization
- can produce sharp image magnified up to 100,000x
104
What are the 2 types of EM and describe them?
Scanning electron microscope (SEM): creates an image by detecting reflected electrons; topology (3D)
Transmission electron microscope (TEM): uses electrons that are passing through thin sections of the sample (transmitted) to create an image
- electron-dense regions appear darker
105
Describe bacterial flagella and their purpose
- bound by motor, rotates allowing organelle to swim
- can detect different organisms via different motors
106
Convert nm/um/mm
200 nm = 0.2 um = 0.0002 mm
0.15 mm = 150 um = 150000 nm
107
What are essential nutrients?
- must be supplied from environment
- macronutrients (large amounts)
- micronutrients (small amounts)
108
Describe and name the macronutrients
- large amounts
- C, N, H, P, O, S
-> carbs, lipids, nucleic acids, proteins
- Mg2+, Fe2+, K+, Ca2+, Na+
-> enzyme cofactors, regulatory molecules
109
What is anabolism?
- build molecules
- endergonic reactions (req. energy)
110
Describe and name the micronutrients
- Co2+, Cu+, Mn2+, Mo2+, Ni2+, Zn2+
-> components of cofactors or enzymes
111
What is metabolism?
catabolism + anabolism
- the energy needed to build cells comes from chemical reactions
112
What is catabolism?
- breaks down molecules
- exergonic reactions (releases energy)
- provides energy for anabolism
113
What nutrients are cycled?
C, N, CO2 and minerals
114
Describe primary producers
(capture essential molecules and build to macromolecules
- biomass forms
- photosynthesize
115
What are consumers?
- grazers (10%)
- predators (1%)
- predators (0.1%)
- all go to decomposers, which recycle back to primary producers in food web
116
What are the two types of autotrophs and describe them?
- photoautotrophs (CO2 as carbon source, energy from photons in sunlight)
- chemoautotrophs (chemolithotrophs) (energy from inorganic chemicals: CO2)
117
What are the two types of heterotrophs and describe them?
- photoheterotrophs (organic compounds and carbon as source of electrons: contradictory and an exception)
- chemoheterotrophs (chemoorganotrophs) (energy from organic chemical compounds, carbon from organic compounds)
118
What are autotrophs as phototrophs and some examples?
- carbon taken from inorganic sources (CO2)
- cyanobacteria, vascular plants
119
What are heterotrophs as phototrophs and some examples?
- carbon from organic compounds
- heliobacteria, most green non-sulfur bacteria
120
What are phototrophs?
Energy taken from sunlight
121
What are autotrophs as chemotrophs and some examples?
- carbon from inorganic sources (CO2)
- sulfur-oxidizing bacteria, hydrogen bacteria
122
What are heterotrophs as chemotrophs and some examples?
- carbon from organic compounds
- most bacteria, animals
123
What are chemotrophs?
- decomposers
- energy from chemical compounds
124
Know carbon cycling diagram
Organotrophy to autotrophy (in week 3 contents)
125
What are diazotrophs?
- convert inorganic N2 (atmospheric nitrogen to ammonium ions
- have nitrogenase enzyme
- alt. called nitrogen fixers
- only few bacteria can fix N2, all life depends on them!
- ex: rhizobium
126
How much of earth's atmosphere is N2?
79%
- unavailable for use by most organism
127
Know nitrogen cycling diagram
w3 content
128
How do most bacteria divide?
- binary fission, parent cell increases in size/cell volume and biomass then splits to two equal daughter cells
- population doubles at each division
129
How do bacteria divide asymmetrically?
- yeast and some bacteria
- asymmetrical budding
- cell does not divide in the middle, daughter cell in one end, forming a bud growing out of one side of mother cell
130
What is generation (doubling) time?
- the time it takes for a population to double
131
What are some environmental conditions?
- pH, temperature, competition with other organisms, nutrient supply
132
What are some physical conditions?
gut pH, pH of infected fruit -> acidic
133
How can we calculate binary fission?
Nt = N0 x 2n
Nt= final cell number
N0= original cell number
n= number of generation
134
What is a fast and slow generation time?
Clostridium perfringens; ~10 minute
typically 20 mins
Mycobacterium leprae (causes leprosy); ~14 days
135
When do bacteria divide at a constant interval?
unlimited & appropriate resources and environmental conditions
136
What are some basics about microbial growth?
- Microbes in nature exist in complex, multispecies communities, but for detailed studies they are grown separately in pure culture.
- measure growth under the optimal nutritional and environmental conditions
- importance of understanding nutrient requirements
137
Explain how some prokaryotes are uncultured and why
- adapted so well to their natural habitats
- some depend on factors provided by other species that cohabit their niche
- some evolved to live inside other cells (intracellular parasites)
- some are obligately symbiotic and cannot grow/survive separated from their partners
138
What are the two main forms of culture media?
- liquid media/broth (cells in suspension)
- solid media (gelled/solidified with agar)
139
What are some applications of liquid media/broth?
- studying the growth characteristics of a pure culture; obtaining large numbers of cells &/or their extracellularly secreted products
140
What are CFU?
- Colony Forming Units
- a visible group of microbial cells that developed from the same mother cell (pure culture)
- liquifies under heat and pressure, solidifies in cool temp
141
What are the applications of solid media?
- trying to separate bacteria in samples e.g. clinical, food, natural environmental samples; isolation of a pure culture (bacterial population grown from a single isolated ‘pure’ colony); studying diversity in a sample, specific traits e.g., colony morphologies, physiology, growth, genetics, antibiotic production, interactions between different bacteria etc.
142
Name the types of microbial culture media?
- complex/rich media
- minimal defined media
- enriched media
- selective media
- differential media
143
Describe complex/rich media
- nutrient rich; exact composition is poorly defined
- ex: contain general extracts of yeast cell, plant and animal tissues
143
Describe selective media
- favour the growth of one organism over another
- ex: high or low pH, plus antimicrobials, specific nutrients
144
Describe minimal defined media
- contain only those nutrients essential for a given microbe's growth
- exact components, known concentrations
145
Describe enriched media
- complex media to which specific factors are added; the microbe is not capable of making them but needs them to grow.
- ex: blood proteins, nucleotides, vitamins, etc
146
Describe differential media
- exploit biochemical/physiological differences between two species that grow equally well (in the medium)
- ex: contain a dye that changes in colour when bacteria produce specific byproducts; differentiate microbes based on their metabolic activities
146
What is the objective and our assumption of dilution streaking and spread plating to isolate of pure cultures?
OBJ: To obtain well isolated single colonies which can be used to establish pure cultures or estimate the total number of bacteria in a sample
ASS: One cell = one colony! (not always true, some bacteria naturally live/occur in pairs or multiples and cannot be separated by these simple techniques)
147
What is MacConkey media?
- to select for ground negatives (ground pos. do not grow)
- used to select for family of gut microbiomes: enterbacteriaceae
- pink when exposed to acidic conditions
- lighter colour (do not produce acid)
147
What are two techniques to isolate pure culture?
- dilution streaking
- spread plating
148
Describe the process of dilution streaking
* Sterilized loop picks up small amount of the sample
* Dragged across surface of an agar plate
* Flame loop to sterilize/kill bacteria, let cool
* Touch to end of the last streak, picking up some bacteria, repeat the streaking
* Flame loop & repeat above steps...
149
What is the result of dilution streaking?
- Dilution of the sample with each streaking set increases the probability of obtaining separation of single bacterium...which upon millions of binary cell divisions produce a visible colony originating from a single bacterium (i.e. a colony forming unit (CFU))
150
What is the goal of diluting spread plates?
* Obtain a dilution that gives nicely separated colonies
* Select plates with ~30-300 Colony Forming Units (CFU)
* Calculate number of bacteria in original sample
150
How do spread plates work for dilutions?
* Set up 10-fold serial dilutions in liquid culture
* A small amount (e.g. 0.1ml) of each dilution is
then plated on agar medium.
151
Why do we care to count microbes?
- Government regulations for food industry, food
handling facilities, health applications, etc.
- Quality control (water safety; contamination;
soil health; etc.)
- Research
152
How can we count microbes?
- must be suspended in liquid to count them (solid samples suspended in liq.)
- expressed as # bacteria/mL of liquid or # bacteria/g of solid
- direct microscopic counts via haemocytometry
- plate counts (dilution plates)
- optical density using a spectrophotometer
153
Describe Neubauer's Chamber of Haemocytometer
- slide under a glass cover
- made of 9 large squares (each large square of 1 mm divided into 25 medium squares of 0.20mm, medium squares divided into 16 small squares of 0.05mm)
153
Describe optical density
- not a measure of cell #, just of culture density
* Microbial cells in liquid suspension increases the turbidity of the liquid; the higher the concentration of the cells the more turbid the suspension
* Measured as light scattered by the suspension at a specific wavelength (usually 600nm) and call the optical density (OD600nm) of the suspension
154
What is the microbial growth cycle?
- analysed as cells density (OD600nm or cell counts) as a function of time
- grown in batch liquid culture (i.e. in a test tube or flask, in a closed system, where media and nutrients are not refreshed)
154
What are the four phases of growth in the microbial growth cycle?
lag, exponential/logarithmic (log), stationary, death
155
Briefly describe the lag phase of the microbial growth cycle
- how do cells respond to their environment?
- bacteria adapt themselves to growth conditions
- bacteria maturing, cannot divide yet
- synthesis of RNA and enzynes
- "bacteria preparing their cell machinery for growth, has to adapt" (when we pick up colony from plate and inoculate it)
156
Briefly describe the exponential/logarithmic (log) phase of the microbial growth cycle
- vegetative growth
- characterized by cell doubling
- if not limited: doubling continues at constant (exponential rate)
- "growth approximates an exponential curve (straight or on log scale)"
- slope of log scale line = number cell divisions/unit time
- growth rates depend on conditions (optimal at time)
- log growth cannot continue indefinitely (medium depleted of nutrients and full of waste)
157
Briefly describe the stationary phase of the microbial growth cycle
- overall population growth plateaus
- due to growth-limiting factors (depletion of nutrients, formation of inhibitory product)
- horizontal linear part of curve
- cells not dead: still create metabolites for survival, no more biomass produced and cells not doubling
- "cells stop growing and shut down their growth machinery while turning on stress responses to help retain viability"
158
What are planktonic cells?
- single cells in suspension
- swarmers: leave to colonize another area
159
What are the two phases of the Exponential/logarithmic (log) phase?
- early exponential: cells grow at max rate possible based on conditions
- late exponential: growth slows due to cell density, initiation of nutrient depletion, accumulation of waste compounds
160
Briefly describe the death phase of the microbial growth cycle
- without new nutrients and/or production of toxic byproducts from dying cells, cells eventially die off
- "cells die with a 'half-life' similar to that of radioactive decay, a negative exponential curve"
161
What does a chemostat ensure?
- continuous logarithmic growth by constantly adding and removing equal amounts of culture medium
- allows growth and growth conditions/environment to be highly controlled
162
Describe feed/effluent for continous culture systems
- feed and effluent inserted at same rate
- constant nutrient accumulation, minimizes waste
- bacteria are mostly happy entire time, can improve/maintain growth rate
163
How could we classify bacteria?
- shapes and arrangement
- how they aggregate together
164
What are some features of a "typica;" prokaryotic cell?
- cytoplasm: gel-like network (70S ribosomes, no mitochondria)
- cytoplasmic membrane
- nucleoid: (packaged bacterial chromosome (1-2), not membrane-bound)
- cell wall: most (not all) have thick complex wall/envelope
- flagellum: only motile bacteria
- may have additional
165
What are pili?
- on surface of many bacteria and archaea
- small "hair"-like protein filaments used for attachment and/or exchange of genetic material
- can transfer DNA, during conjugation/mating (they bind other microbes), from donor to recipient
- pathogens adhere to host cells and initiate disease
166
What are sex pili?
- aka conjugation pili
- type of pili
- long, hollow, filamentous extensions from cell surface
167
What are fimbriae?
- shorter versions of pili (also hollow, shorter tubes)
- used for adhesion (pathogens adhere to host cells and initiate disease)
168
What are stalks?
- some bacteria form them as attachment organelles
- extensions of cell envelope and cytoplasm
- Secretes adhesion factors to “anchor” bacterium in environment (Caulobacter crescentus)
- Allows formation of biofilms in water streams
169
What are flagella?
- some bacteria and archaea
- Long, helical appendages extending from cell membrane; whip-like; used for motility
- we can test where flagella are present (indirect process)
- different arrangements that allow you to tell different organisms apart?
169
What are the different arrangements for flagella and describe them?
- atrichous (no flagellum)
- monotrichous (1 flagellum out of one end)
- amitrichouse (1 flagellum out of both ends)
- lophotrichous (many flagella out of one end)
- petrichous (many flagella coming out of many parts of cell)
- amphilophotrichous (many flagella coming out of both ends)
170
What is prokaryotic genetic material made of?
- irregular shaped region within cell hat
- 1-2 chromosomes (typically circular and haploid)
-> organized into a series of supercoiled domains by DNA-binding proteins called Nucleoid-Associated Proteins (NAPs) to form the nucleoid
-> our nucleus has approx 2m DNA that is packaged into condensed microns
- plasmids
-> extrachromosomal DNA; small, circular, double-stranded DNA molecules, activity is DNA targeted-
171
Desscribe genomes (prokaryotes) as prokaryotic genetic material
- compact genomes with very little non-coding DNA
- bacteria does not always have circular chromosomes
- range of sizes
- count chromosomes size: where the chromosome starts replicating; how many nucleotides there are
- bulk of DNA encloses something, has high coding capacity (no junk-non-coding DNA associated)
172
Describe plasmids as prokaryotic genetic material
- found in archaea, bacteria, and some eukaryotic microbes
- extra-chromosomal DNA elements, usually circular, that replicate autonomously (do not need to replicate when genome of cell does; variety of genetic info)
- typically much smaller than chromosomes
- copy number per cell varies widely (depending on plasmid and its location)
- Contains additional/advantageous genetic information, typically not required for “every day” prokaryotic survival (e.g., genes encoding antibiotic resistance, toxins)
- non-essential for support of cell
173
What is Horizontal gene transfer (HGT)?
- the transfer of genes between organisms, outside of traditional reproduction
- Occurs almost exclusively in prokaryotes
- replicates in straight line
174
What is vertical gene transfer?
- the transmission of genes from the parental generation to the offspring by asexual reproduction (binary fission)
- meiosis
175
What are some mechanisms of genetic diversification?
Transformation, transduction, conjugation
- asexual bacteria transfer
- do not sexually reproduce like meiosis cross over (recombination)
175
Describe transformation as a mechanism of genetic diversification
- allows cells to uptake DNA from environment
- can acquire antimicrobial resistance
fragmented: can enter another cell's genome
- takes up anything present
176
Describe transduction as a mechanism of genetic diversification
- allows DNA to transfer through bacteriophages (phage) that infect bacteria
- range of bacteriophage specificity is narrow: within species or close relative due to the way phages bind, range of specificity based on phage; more narrow
- phages duplicate viruses, take bacterial genome with it + genetic material
176
Describe conjugation as a mechanism of genetic diversification
- allows bacteria to directly transfer DNA between cells via pili
- Do not have to be the same species to exchange DNA!
- donor cell does not lose information (replicated)
177
What are transposons, referenced to conjugation as a mechanism of genetic diversification?
- fragments of DNA that can move within genome (jumping DNA fragments), moves DNA around within genome
- can be integrated into fragments
sex pilus binds to recipient cell, which moves plasmids into recipient, causing it to have the same traits of donor cell
178
Briefly describe the fluid mosaic model
- membrane composed of phospholipid bilayer with embedded proteins
- Proteins are the gatekeepers and perform multiple functions
- Phospholipids layer prevents free movement across membrane of polar or charged molecules, proteins facilitate transport
- The abundance, diversity, composition and arrangement of proteins and lipids vary with growth conditions and between species
179
Briefly describe the features of the fluid mosaic model
integral proteins: membrane spanning, form intercellular pathways, function as receptors, transporters/permeators (channels)
peripheral proteins: bound to cytoplasmic side of membrane, to phospholipids or integral proteins
phospholipids: anchored in membrane; bound to protein
- proteins can be modified when sugar is added to theme
180
Describe phospholipids in the fluid mosaic model
- anchored in membrane; bound to protein
- amphipathic molecules
- Polar/charged (hydrophilic) head orient towards
aqueous environment
- Hydrophobic tails orient away from water
181
Describe unsaturated fatty acid chains
- melt at lower temp
- increase fluidity; saturated lipids compress at low temp, press together, making a dense and rigid membrane
181
Describe saturated fatty acid chains
- melt at high temperatures
- increase order/rigidity
181
How are membrane lipids diverse from different cells?
- phospholipids vary with respect to their phosphoryl head groups (ethanolamine, glycerol, etc.) and their fatty acid side chains
- fatty acid chains: saturated, unsaturated, polyunsaturated, may contain cyclic structures
- Membranes of microbes that live at low temperature have higher abundance of unsaturated lipids
182
What are sterols?
- reinforcing agents in eukaryotic membranes
- provide structure and rigidity to membrane, supports functionality of membrane
- cholestorol
- planar molecules that fill gaps between hydrocarbon chains to control membrane structure
182
What are hopanoids/hopanes?
- similar to sterols in eukaryotic membranes
- carries out the same function as sterols but in bacteria
182
How do prokaryotes regulate membrane fluidity and rigidity?
- varying the abundance of these different membrane lipids and hopanoids
183
How do archeal lipid tails differ?
- kong isoprene chains with a methyl sidechain every 4 carbons
- Bacteria: straight chains of fatty acid without branches
183
What are the bonds that joinds the lipid tail to the glycerol?
Archaea: glycerol-ether-lipids
Others: glycerol-ester-lipids
* ether is stronger than ester bonds, take more energy to break, much more stable at high temperature
183
Describe a monolayer membrane in some archaea
- Tails of two phospholipids fused into a single molecule with two polar heads
- may make membranes more rigid to resist harsh environments
183
What is the mirror image (enantiomer) of bacteria?
- stereochemistry of archaeal glycerol moiety
184
Explain the permeability barrier in prokaryotes
- prevents leakage and functions as a gateway for transport of nutrients into/out of cell
- cell membrane is diffusion barrier (separates internal cell environment from external environment)
184
What does the Prokaryotic Cytoplasmic membrane serve as?
- site to anchor proteins
- site of proton motive force for energy conservation
- Protects/encloses the cytoplasm and its content, selectively facilitates transport in and out of the cell/cytoplasm
184
What are the 3 types of additional envelope layers in most bacteria?
- they provide structural support and protection
- gram-positive bacteria: thick cell wall (peptidoglycan)
- gram-negative bacteria: thin cell wall (peptidoglycan)
- mycobacteria (complex, multilayered cell wall- no outer membrane: mycolic acid interspersed with phospholipids, giving it thick and rich bilayer; impermeable to various molecules and predators/environment)
185
What are most bacterial cell walls (sacculus) made of?
- peptidoglycan sugar chains (linked by AA) (aka murein) and cross-bridges
- repeating disaccharide unites, adjacent polymers are cross-linked
- Peptidoglycan consists of alternating units of N-acetylglucosamine (NAG) and N- acetylmuramic acid (NAM)
185
What does N-acetylmuramic acid bond to?
- short peptide (4-6 amino acids)
185
How do peptides cross-link?
- via bond between D-Alanine and m-Diaminopimelic acid
- connecting the parallel glycan strands
186
How does vancomycin and penicillin work in trans-peptidase?
- vancomycin binds to d-ala-d-ala and blocks cross-bridge formation
- peptide cross-bridge forms with release of d-alanine, blocked by peniccilin
- terminal d-alanine released
186
What does peptidoglycan help with?
- confer cell shape
Peptidoglycan
- withstand turgor pressure (osmotic pressure arising from the cytoplasm and pressing against the cytoplasmic membrane; plants)
187
How is peptidoglycan unique to bacteria relative to 2 antibiotics?
penicillin: inhibits the transpeptidase that cross-links the peptides (B-lactamases break penicillin; antibiotic has no functionality)
vancomycin: prevents cross-bridge formation by binding directly to the D-Ala-D-Ala (prevents release of d-ala; binds dimer)
- excellent target for antibiotics
188
How does peptidoglycan vary in gram-positive bacteria?
- short (tetra)peptides of peptidoglycan chains
- linked by bridges of pentapeptides made of glycines (pentaglycines)
- multiple layers of peptidolgycan
189
What is peptidoglycan threaded with in gram-positive bacteria?
- teichoic acids: glycerol phosphate and carbohydrates (phosphodiester-linked glycerol with sugars or amino acids bound to central glycerol -OH)
- lipoteichoic acids: bound to phospholipids as reinforcement (added strength and rigidity)
190
What are the pros of gram-positive bacteria?
- strong: very thick cell wall with lipoteichoic acids and teichoic acids thread through it adding strength
- Protection against osmotic lysis
- Gram-stain purple
190
What are the cons of gram-positive bacteria?
- Susceptible to lysozyme and other things that attack the cell wall, which is readily accessible
- More susceptible to antibiotics than Gram-negative bacteria
191
Describe the membranes in gram negative bacteria
- separated by periplasm (space between two membranes) that contains peptidoglycan
- thin peptidoglycan layer consists of one or two sheets
OUTER:
- Outward-facing membrane containing
lipopolysaccharides (LPS)
- Contains transmembrane proteins called porins (act as a pore, through which molecules can diffuse)
- Lipoproteins that anchor peptidoglycan in
place
INNER/CELL:
- proteins functionally distinct from those in outer membrane
192
What is LPS (lipopolysaccharide) in gram negative bacteria?
- major permeability barrier in outer membrane
- act as endotoxin = molecules that are harmless when pathogen is intact, but become toxic and activate immune response when it is released from a lysed cell
- complex glycolipid with 3 distinct
parts/regions
- O-antigen: repetitive polysaccharide (the
composition varies from strain to strain), enormous variation, inserts into membrane very stable binds
- Core polysaccharide (conserved within organisms)
- Lipid A anchors core polysaccharide in the outer membrane
193
Describe LPS and serotyping in gram-negative bacteria
- LPS is one of most structurally variable macromolecules on Earth
- Used for classification of pathogens species = called serotyping (e.g., E. coli O157:H7)
- Different compositions of LPS among the same species of pathogen = different serovars (strains) of the same pathogen
194
Describe serotyping; what does O and H mean of ex: E. coli O157:H7
O- specific O antigen for LPS
H- what antigens are present on the flagella
195
What are the pros of gram negative bacteria?
* The outer membrane is an excellent selective permeability barrier
* Able to defend itself against a wide range of toxic molecules
* Peptidoglycan is protected
* Stains pinkish-to-reddish with the Gram stain
195
What are the cons of gram negative bacteria?
* Is energetically expensive to build and maintain (need extra material)
* Usually have larger genomes – genes for outer membrane components
- significant exposure for haploid org. in nature: prokaryotic, some eukaryotic (yeast)
196
What are some distinguishing characteristics of the mycobacterial cell wall?
- thicker than many prokaryotes
- hydrophobic, waxy mycomembrane
-> rich in mycolic acids (component unique to mycobacteria); contains 2 HC chains (1 short, 1 long), interleaved with sugar mycolates (dense)
-> final outer layer of hydrophobic phenolic glycolipids
- Mycolic acid layer and a peptidoglycan layer held together by the polysaccharide, arabinogalactan* (arabinose and galactose)
- Characterized and stained using the Ziehl-Neelsen acid-fast stain that targets mycolic acids; important diagnostic test
197
Describe the mycobacteria envelope structure (mycomembrane)
- thin peptidoglycan with lots of liquids
- difficult for grams to pass
- HC chains bind to sugar molecules, bound to lipids that are branched, interspersed with previous mycolic acids; repeated
- thick hydrophobic lipid layer on top of sugar molecules
- sugars (link together) that binds to peptidoglycan
198
What are the pros of mycobacteria?
- Thick, waxy outer mycomembrane
- Resistance to: dryness, osmotic stress, wrinkles, detergents, antiseptics, many antibiotics (especially hydrophilic ones), phagocytosis by host defence cells, killing by host immune defenses
199
What are the cons of mycobacteria?
- grows slowly
- cell envelope is energetically expensive to synthesize and maintain thick cell wall
200
What is an S (surface)-layer?
- most archaea, some bacteria
- Consists of a monomolecular layer of identical proteins or glycoproteins
encloses the whole cell surface
- Prokaryotic ”exoskeleton/chainmail”; 5-25 nm thick
- Fit together like tiles in highly ordered array
- protective layer (covers entire cell)
- the outermost line in a electrongraph
200
What are some diverse functions of the surface-layer in the prokaryotic cell wall?
- Can flex and central pores in subunits allow movement of molecules
- Additional external-most protective layer against osmotic stress, viruses & predators
- Assists adherence and biofilm formation
201
Describe the archaeal cell wall
* Semi-rigid structure for protection (like Bacteria) - No peptidoglycan (unlike Bacteria)
- Archaea have variety of cell wall types; adapted for specific environment; some archaea lack cell walls entirely
202
Describe the proteinaceous S-layer in archaeal cell walls
- considered a part of the call wall (unlike Bacteria)
- Often anchored to cell membrane
- In some species S-layer is the only cell wall component
- Some species contain a protein sheath in addition to the S- layer
203
Describe pseudomurein in archaeal cell walls
pseudopeptidoglycan
- a few species
- with N-acetylalosaminuronic acid (NAT) rather than NAM; forms stronger peptide interbridges
203
Describe methanochondroitin in archaeal cell walls
- cell wall polymer in some archaea
- Similar to connective tissue component (chondroitin) in vertebrae
- sugar that forms monomer, structure slightly different than peptidoglycan
- adds to structural integrity
204
What are the functions of the prokaryotic cell wall?
● Protection against the immune system; prevent phagocytosis (encapsulated is dangerous)
● Assist with adherence
● Protection from dehydration
205
Describe capsules on the prokaryotic cell wall
- can occur on Gram positive or Gram negative bacteria
- can secrete polysaccharides that would present outside cell walls
- Additional cell capsule exterior to cell wall
- Consists of a coat of polysaccharides and glycoproteins loosely bound to the cell envelope, bind water; form a hydration layer
- Difficult to stain, thus appears as ‘halos’ around cells
- May exist along with S layers; if so, found external to the S-layer
206
Describe phylum cyanobacteria
- oxygenic (product oxygen)
- photoautotrophic prokaryotes
- Earth’s atmospheric oxygen comes from cyanobacteria and plant chloroplasts that evolved from an ancient cyanobacterium
- Contains chlorophyll and associated pigments
-> Cyanobacteria commonly appear green because of predominant blue and red absorption by chlorophylls a and b
-> The phylum Cyanobacteria (sometimes called ‘blue-green algae’) is named for the blue phycocyanin accessory pigments possessed by some genera
206
Describe bacterial diversity
- prokaryote (Domain Bacteria and Domain Archaea) microbes have evolved an amazing array of life forms that colonize every habitat on Earth
- grows everywhere
- Prokaryotes share some major common traits; however, there is great diversity within and between members of each domain
- Each Domain has multiple Phyla, which contain multiple Classes, Orders, Families, Genera, species
- bacteria taxa have different evolutionary paths and have evolved complex traits and often unclear borders (i.e. complex & unclear taxonomy!) (differentiate very quickly)
207
Name the best studied phyla of domain bacteria
- Oxygenic phototrophs: Cyanobacteria
- Gram-positive: Firmicutes & Actinobacteria
- Gram-negative: Proteobacteria
- Gram-negative: Spirochetes, Bacteroidetes
- PVC Superphylum: Planctomycetes, Verrucomicrobia, and Chlamydiae
207
Describe encapsulate forms of capsules
- dangerous
- slimy
- density associate with it due to nature of molecules- polysaccharides
- difficult for stains to get through; use india ink to get clear halos around cell
208
What are CO2-fixing enzymes?
- very specific
- function within Calvin cycle
- ex: rubisco
208
What are specialized protein microcompartments?
ex: carboxysomes
- Found in Gram negatives
- Characteristic polyhedral-shaped selectively permeable protein shell containing CO2–fixing enzymes
- Found in all cyanobacteria as well as some chemotrophs that fix CO2
208
What are thylakoids?
- only available for Gram-negative phototrophs (energy from light/photons; e.g., cyanobacteria)
-> Specialist systems of extensively folded lamellae (sheets) of membranes
-> Packed with chlorophyll, photosynthetic proteins and electron carriers
-> Maximize photosynthetic capability of the cell
209
What is Prochloroccus marinus?
* Marine cyanobacteria; one of the most plentiful organisms on Earth
* Responsible for production of ~20% of oceanic photosynthesis!
209
Describe gas vesicles as a specialized structure
- allows microbes to float; aquatic phototrophs and some aquatic heterotrophs
- typically aqueous, in water environments
210
What are specialized structures?
- specialized within bacteira, polyhedral, permeable (molecules go in/out), made of rubisco, enzyme in very high conc.
211
What is cyanobacterium Microcystis?
- Hollow protein tubes with conical ends packed into
hexagonal arrays
- Collect gases produced by metabolism (e.g., H2, CO2)
- Allow a microbe to maintain a set buoyancy optimal to its preferred conditions in the water column; allows microbes to remain afloat
- specific depth (to be in touch w sunlight) to accept spec. wavelengths of energy levels, so chloroplasts can take energy, need to float; to photosynthesize
212
Describe the implications of toxic microcystic algal
- toxic versions bloom in lakes (lake eerie); caused by waste water and agricultural pollution, leading to overgrwoth and algal bloom formation
- they secrete toxins, toxic to us and other organisms, damages lake from life it supports and people that use it
212
What is the cyanobacterial cell structure, and how do specialized structures affect it?
* Conduct photosynthesis in THYLAKOIDS (membrane- bound compartments inside cyanobacteria)
* Fix CO2 in CARBOXYSOMES (bacterial microcompartments filled with the enzymes
ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) used in carbon fixation)
* Maintain buoyancy using GAS VESICLES
* Many fix N2 in specialized cells called HETEROCYSTS
213
Which cyanobacteria are toxic?
- some are blue or green, some have red pigments
- some cyanobacteria produce highly potent toxins that can be secreted into water, causing toxic effects for humans and animals
- ex: algal blue: very potent and stable
213
Describe some real life versions of cyanobacteria?
red pigments: flamingos get their colour from a cyanobacteria diet
- can be used as food/dietary supplement (increasing popularity)
- used as human and animal food source
- production of eco-friendly renewable biofuels
- filed products: lipids of high value
214
How can we classify microorganisms based on environmental conditions?
temperature, pH, osmolarity, oxygen, pressure
215
**What are facultative anaerobes?
can grow in any oxygen-related conditions, but can only use aerobic respiration
- respiration: it can deal with ROS
- can switch to fermentation if no oxygen present
215
**What are aerotolerant anaerobes?
- tolerate oxygen, but don’t metabolize it
- they suffer no toxic content of organisms
- can grow anaerobic,
- grow in oxygen and no oxygen situations, but can only use anaerobic respiration
215
**Describe microaerophiles
- must use oxygen to generate energy, but high concentration of it kills them
- can’t ferment or in anaerobic condition
215
Describe aerobic and anaerobic respiration
- electron transport system generates ATP (ET chain+ATP synthesis)
- aerobic (humans, O2) -> Reactive Oxygen Species generated; toxic; enzymes (dismutases, catalases) deal with these; detoxify
- anaerobic respiration (use ETC, anything other than O2; NO3-, SO4-, FE3+
216
What is fermentation?
- glycolysis generates ATP
216
What are barophiles?
- organisms under high pressure
217
What are superphylum proteobacteria?
- proteobacteria has 5 major classes considered to be phyla- alpha-, beta-, gamma-, delta-, epsilon- proteobacteria
- spectrum of groupings within proteobacteria
- gram-negatives
- all share common structure: triple-layered Gram-negative cell envelope: outer membrane, thin peptidoglycan, periplasm
- diverse metabolism and lifestyles
218
What are the possible diverse metabolisms of superphylum proteobacteria?
- fermentation
- aerobic & anaerobic respiration: heterotrophs, photoheterotrophs
219
What are the possible diverse lifestyles of superphylum proteobacteria?
- single free-living in various habitats
- in symbiosis with plants and animals
- some are pathogens
- plats into dif. symbiotic relationships
220
What are phylum alphaproteobacteria?
- type of proteobacteria
Endosymbionts: Nitrogen fixers and plant roots including Rhizobium
- As isolated bacteria, they are generally rod- shaped with aerobic metabolism.
- Within the host cells, the bacteria lose their cell wall and become rounded bacteroids, specialized for nitrogen fixation.
- The host plant cells provide the bacteroids with nutrients
- exchange nitrogen for carbon made for plant
221
What are phylum gammaproteobacteria?
- type of proteobacteria
- include enteric bacteria that colonize the colon
- Gram negative rods; motile by flagella; tolerant to bile salts (mcconkey agar); facultative anaerobes & fermentation
- include many species pathogenic to humans and animals (many are also not)
222
What are phylum gammaproteobacteria?
- type of proteobacteria
- non-sport forming, gram-negative rods, aerobic and anaerobic species
- can be opportunistic pathogens; mostly commensals (beneficial to human host)
- Break down toxins in food
223
What are the distinct phylogenetic branches of gram positive bacteria?
- phylum firmicutes (thick peptidoglycan; low-GC species)
- phylum actinobacteria (high-GC species)
223
Describe phylum firmicutes in the genus bacillus
- Consists of large rod-shaped cells
EX: B. subtilis = A “model system” for Gram positives
EX: B. anthracis = found in soil, causative agent of anthrax
- Vegetative cells develop inert endospores in times of starvation and stress.
- Released spores germinate in favourable conditions
- pores formed asexuall
224
Describe phylum firmicutes in the genus clostridium
- Rod-shaped cells, form endospore which swell, forming a “drumstick.”
- Habitat: soil, can contaminate foods
EX: C. botulinum; Botox is used to relax muscle spasms.
225
What are some non-spore-forming firmicutes?
- staphylococcus
- streptococcus
within soil and other areas of nature
226
Describe staphylococcus
- Facultative anaerobes
- Cocci in clusters
- Staphylococcus aureus (S. aureus)
§ Methillicin-resistant Staphylococcus aureus (MRSA)
226
Describe streptococcus
- Aerotolerant
- Cocci in chains
- Streptococcus pneumoniae
- S. pyogenes
227
What is phylogeny based on?
both the small subunit 16S rRNA and genome sequences
227
What is the phylogeny of domain archaea?
* Diverged from the evolutionary branch that gave rise to eukaryote
* Found in many environments; many species live under extreme conditions (extremophiles); grow within a wider range of:
-> Temperature, Osmolarity, pH, other environmental conditions
* Several taxa group into superphyla
-> Euryarchaeota – most divergent
227
What does polyphyletic mean?
- ancestor not in group
228
What are methanogens?
- euryarchaeota have many several polyphyletic clades of them
- Serve a key energetic role in ecosystems for anaerobic removal of H2 and other reductants; produce methane
- Basic reaction CO2+4H2→CH4+2H2O
229
What are the environmental niches of euryarchaeota methanogens?
-soil, under permafrost, in ruminant / animal digestive tracts, landfills, and in marine floor sediment
- A major methanogenic environment is the anaerobic soil of wetlands, especially rice paddies; landfills
230
What do methanogens cause?
- produce methane deep underground
- tapped in ice as methane hydrates under
oceans of in permafrost
- large amount of methane is trapped in a crystal structure of water, forming a solid similar to ice
231
What is global warming doing to permafrost?
- melt, releases CH4 (massive problem)
- CH4 is >20 times more potent as greenhouse gas than CO2
- CH4 is cleanest burning natural gas
- can be energy source if used more effectively
- Bovine methanogenesis makes a significant contribution to global methane
232
Describe thermophiles
- euryarchaeota
- like temps 50-80°C; can be bacteria or Archaea
- Hyperthermophiles like temps >80°C, are almost always Archaea
- Habitat often represent multiple extreme conditions
232
Describe the structure of methanogens
- archaea: rigid cell walls made of pseudopeptidoglycan, sulfated polysaccharides or proteins; S layer
- morphologically diverse
- rods (single or filamentous), cocci, spirals
232
Give an example of a hyperthermophile
- Pyrococcus furiosus
- Lives in deep-sea in hydrothermal vents
- barophile
- Can only survive at temps >70°C (prefers 100°C)
- An anaerobe that metabolizes sulfur to H2S
- small, withstand high P
- something made within cell allowing them to strengthen cytoplasm
232
How have we used archaea in biotechnology?
- Extremophiles make enzymes with novel ranges of stability “extremozymes”
- PFU; more stable, faster acting, less errors than TAQ for DNA amplification
- archaeal lipids are good vaccine adjuvants
- source of novel antibiotic classes being explored by pharmaceutical industry
