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YR2SEM1 > Microbio 1/2 > Flashcards

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
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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
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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)
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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
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5
Q

What can the naked eye see?

A

up to 200nm
- microbes are around 5nm

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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
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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’
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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
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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
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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
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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
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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
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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
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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

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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

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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
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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
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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

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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)

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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
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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
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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”)
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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)
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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
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25
Q

Who was Dmitri Ivanovsky?

A
  • discovered a disease-causing agent so small that it passed though 0.1 μm pores in a filter
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26
Q

Who was Martinus Beijerinck?

A

proposed the filtrable agent was not a bacterium; it was a novel unknown microbe coined ‘virus’ (latin for poison) (because they infect something)

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27
Q

Who was Wendell Stanley?

A

later purified & crystallized the agent & using electron microscopy identified the Tobacco Mosaic Virus (TMV)

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28
Q

Why was the “Spanish Flu” an inaccurate name for the influenza pandemic during WW1?

A

Spain did not contribute to world w1, they reported the deaths but did not start the flu

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29
Q

How did WW1 speed up the pandemic’s progress?

A

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

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30
Q

Who was Sir Alexander Fleming?

A
  • scottish medical researcher living in britain
  • ## finds mould Penicillium notam inhibits growth of Staphylococcus bacteria, isolates “penicillin”
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31
Q

Who was Mary Hunt?

A
  • 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
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32
Q

How did life expectancy increase?

A
  • increased sanitation and hygiene
  • later: discovery of antimicrobial drugs and vaccines
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33
Q

What are a concern about global and infection + diseases?

A
  • 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.)
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34
Q

What is another concern about global and infection + diseases?

A
  • Population density & Globalization
    -> earth growing at a tremendous state
    -> growing population density can spread diseases faster
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35
Q

What is a third concern about global and infection + diseases?

A
  • 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
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36
Q

What is the AMR crisis? (Antimicrobial drug resistance)

A
  • 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
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37
Q

Do all microbes cause disease?

A
  • no, most do not and they are essential to all aspects of life on the biosphere
  • arose with the development of new technologies
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38
Q

How is human health affected by infection and diseases?

A
  • 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
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39
Q

What is fermentation?

A

occurs in absence of oxygen, microbe thrives as they want energy to grow

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39
Q

Why do people eat kombucha and kimchi?

A
  • to sustain health of the gut microbiome, makes metabolize
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40
Q

How are prokaryotes different from eukaryotes?

A
  • 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)
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41
Q

What is the cell wall made of in bacteria, fungi, and plants?

A

bacteria = peptidoglycan
fungi = chitin (deadly to humans)
plants = cellulose

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42
Q

What does phototrophic mean?

A

can synthesize (make their own energy from sunlight)
- bacteria, plant, algae

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43
Q

What does heterotrophic mean and what are some examples?

A
  • they get energy from simple sugars (do not synthesize their own)
    bacteria + fungi + mammals + protists
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44
Q

What does phylogenetic mean?

A
  • Evolutionary development (descent) and diversification of organisms from a common ancestor
  • divergencies
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45
Q

What is the endosymbiont theory?

A
  • explains origin of eukaryotic cells from prokaryotic organisms
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46
Q

What did mitochondria and chloroplasts descend from?

A
  • 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
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47
Q

What are 4 non-beverage fermented food products?

A
  • yogurt
  • pickles
  • tofu
  • bread
    etc
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47
Q

What are 4 concerns regarding infection and diseases?

A
  • global warming/climate change
  • population density + globalization
  • changing susceptibilities of diseases
  • antimicrobial resistance
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48
Q

Who was Carolus Linnaeus (1701-1778)

A
  • 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)
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49
Q

What is the taxonomic hierarchy of classification?

A
  • hierarchy of groups of related organisms (taxa) based on successively narrow criteria
  • now based on DNA sequence similarity
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49
Q

What is the sequence of taxons

A

domain > division (phylum) > class > subclass > order > family > genus > species

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50
Q

How can we define a species?

A
  • 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)
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51
Q

How do we write species names?

A
  • write genus and species
  • genus is always capitalized, species is never
  • written in italics
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52
Q

Describe bacteria

A
  • 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
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53
Q

What are some bacteria examples?

A
  • 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)
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54
Q

Describe archaea

A
  • 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
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55
Q

Give some examples of archaea (the conditions they live in and real-life implications)

A
  • 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.
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56
Q

What are domain eukarya? (4)

A
  • protists
  • fungi
  • plants
  • animals
  • eukaryotic cell structure, defined nucleus
  • typically larger than bacteria
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57
Q

What are protists?

A
  • anything except plants, animals, or fungi
  • so many; cannot efficiently categorize them
  • can live as single cells or in larger multicellular communities
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58
Q

What is algae?

A
  • broad characteristic of protists
  • unicellular or multicellular and vary widely in size, appearance, and habitat
  • cell walls: cellulose
  • photosynthetic !!
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59
Q

What is protozoa?

A
  • broad characteristic of protists
  • very diverse
  • move with cilia/flagella
  • some photosynthetic, parasitic, pathogenic
    ex: paramecium
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60
Q

What are fungi?

A
  • 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
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61
Q

What are yeasts?

A
  • unicellular
  • Large impacts in food production & safety
  • Can cause gonadal infections and oral thrush
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62
Q

What are Molds / filamentous fungi?

A
  • 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
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63
Q

What are viruses?

A
  • 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
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64
Q

What is a petri dish?

A

flat-lidded dish that is typically 10–11 centimeters (cm) in diameter and 1–1.5 cm high

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65
Q

What are test tubes?

A

sterile, capped cylindrical plastic or glass tubes with rounded bottoms
- sterilized by autoclaving

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66
Q

What is a bunsen burner?

A
  • metal apparatus that creates a flame burning gas
  • used to sterilize pieces of equipment
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67
Q

What is an inoculation loop?

A
  • 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
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68
Q

What happens if we do not sterilize the inoculation loop?

A

whatever growing in lab would stick to it and affect the plate
- sterilized when put into bunsen burner (working aseptically)

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69
Q

What are microscopes?

A
  • produce magnified images of microorganisms, human cells and tissues
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70
Q

What are stains and dyes?

A
  • add colour to microbes so they can be better observed
  • fixation may be required
  • cellular chemical composition
  • dye bonds to structure and cells
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71
Q

What is growth media?

A
  • 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
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72
Q

What can we see with a light microscope?

A
  • generally: bacteria, archaea, yeasts
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73
Q

What is light, generally?

A
  • match microorganisms to grow to their required nutrients
  • wavelength (lambda) increases, energy decreases
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74
Q

What does resolution require?

A
  • 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
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75
Q

How does light interact with an object?

A

absorption, reflection, refraction, scattering

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76
Q

Describe light microscopy

A

resolves images according to absorption of light

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77
Q

Describe electron microscopy

A

uses beams of electrons to resolve smaller details (smaller than the wavelength of visible light)

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78
Q

Describe atomic force microscopy

A

uses intermolecular forces to map 3D- topography of the cell

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79
Q

Describe X-ray crystallography

A

detects the interference patterns of X-rays entering the crystal lattice of a molecule

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80
Q

What are the 4 types of light microscopy?

A
  • Bright field microscopy
  • Dark field microscopy
  • Phase-contrast microscopy
  • Fluorescence microscopy
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81
Q

Describe resolution

A
  • 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.
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82
Q

Describe contrast

A
  • difficult to distinguish small structures in microorganisms due to transparency
  • mechanisms to increase contrast to resolve detect different structures
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83
Q

Describe magnification

A
  • the ability of a lens to enlarge the image of an object when compared to the real object
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84
Q

What is the numerical Aperture (NA)?

A

higher the NA, the higher the resolving power of the objective

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85
Q

What is a compound microscope for light microscopy?

A

Has a system of multiple lenses designed to focus, correct and/or compensate for aberration of the objective
- has ocular lenses and objective lenses

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86
Q

List the features named on lenses

A

magnification (x10..), numerical aperture (/1.25), immersion objective (oil)

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87
Q

How can we find the total magnification?

A

__X ocular lens & __X objective
10x x 100x
= 1000x

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88
Q

Describe oil immersion and why we choose it

A
  • 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
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89
Q

What are the advantages and disadvantages of bright field microscopy and staining?

A

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)

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90
Q

What is bright field microscopy?

A
  • most common type of light microscopy
  • object appears as dark silhouette, blocking passage of light
  • resolution limit is approx 1000x
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91
Q

What is a wet mount and how do we properly apply it?

A
  • a drop of water on a glass slide with a coverslip
  • start on angle and then slowly drop slide so no air bubbles
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92
Q

What is the difference between a simple and differential stain?

A

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 !

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93
Q

What is gram-positive bacteria?

A
  • retain the crystal violet stain because of thicker cell wall, cells appear purple
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94
Q

What is gram-negative bacteria?

A
  • bacteria do not retain the stain, cells appear a pinkish/reddish colour
  • thin cell wall
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95
Q

What is acid-fast staining?

A
  • differentiate two types of gram-positive cells (those with waxy mycolic acids in cell walls and those that do not)
    *know method !
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96
Q

What is capsule staining?

A
  • 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)
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97
Q

What is endospore staining?

A

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

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98
Q

What are the 4 different types of staining?

A

endospore, capsule (negative), acid-fast, gram
+ simple with methylene blue

  • know each method
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98
Q

What is phase contrast microscopy?

A
  • 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
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99
Q

What is fluorescence microscopy?

A
  • tool for detecting parts of cells
  • specimen absorbs light of defined wavelength, emits light of lower energy (longer wavelength), specimen fluoresces
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100
Q

What is autofluorescence in fluorescence microscopy?

A
  • some cell components naturally fluoresce under specific light wavelengths; no stain required
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101
Q

What are fluorophores in fluorescence microscopy?

A
  • 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)
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102
Q

What is immunofluorescence?

A
  • 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)
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103
Q

How is an electron microscope better than light microscopy?

A
  • 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
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104
Q

What are the 2 types of EM and describe them?

A

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

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105
Q

Describe bacterial flagella and their purpose

A
  • bound by motor, rotates allowing organelle to swim
  • can detect different organisms via different motors
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106
Q

Convert nm/um/mm

A

200 nm = 0.2 um = 0.0002 mm
0.15 mm = 150 um = 150000 nm

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107
Q

What are essential nutrients?

A
  • must be supplied from environment
  • macronutrients (large amounts)
  • micronutrients (small amounts)
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108
Q

Describe and name the macronutrients

A
  • large amounts
  • C, N, H, P, O, S
    -> carbs, lipids, nucleic acids, proteins
  • Mg2+, Fe2+, K+, Ca2+, Na+
    -> enzyme cofactors, regulatory molecules
109
Q

What is anabolism?

A
  • build molecules
  • endergonic reactions (req. energy)
110
Q

Describe and name the micronutrients

A
  • Co2+, Cu+, Mn2+, Mo2+, Ni2+, Zn2+
    -> components of cofactors or enzymes
111
Q

What is metabolism?

A

catabolism + anabolism
- the energy needed to build cells comes from chemical reactions

112
Q

What is catabolism?

A
  • breaks down molecules
  • exergonic reactions (releases energy)
  • provides energy for anabolism
113
Q

What nutrients are cycled?

A

C, N, CO2 and minerals

114
Q

Describe primary producers

A

(capture essential molecules and build to macromolecules
- biomass forms
- photosynthesize

115
Q

What are consumers?

A
  • grazers (10%)
  • predators (1%)
  • predators (0.1%)
  • all go to decomposers, which recycle back to primary producers in food web
116
Q

What are the two types of autotrophs and describe them?

A
  • photoautotrophs (CO2 as carbon source, energy from photons in sunlight)
  • chemoautotrophs (chemolithotrophs) (energy from inorganic chemicals: CO2)
117
Q

What are the two types of heterotrophs and describe them?

A
  • 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
Q

What are autotrophs as phototrophs and some examples?

A
  • carbon taken from inorganic sources (CO2)
  • cyanobacteria, vascular plants
119
Q

What are heterotrophs as phototrophs and some examples?

A
  • carbon from organic compounds
  • heliobacteria, most green non-sulfur bacteria
120
Q

What are phototrophs?

A

Energy taken from sunlight

121
Q

What are autotrophs as chemotrophs and some examples?

A
  • carbon from inorganic sources (CO2)
  • sulfur-oxidizing bacteria, hydrogen bacteria
122
Q

What are heterotrophs as chemotrophs and some examples?

A
  • carbon from organic compounds
  • most bacteria, animals
123
Q

What are chemotrophs?

A
  • decomposers
  • energy from chemical compounds
124
Q

Know carbon cycling diagram

A

Organotrophy to autotrophy (in week 3 contents)

125
Q

What are diazotrophs?

A
  • 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
Q

How much of earth’s atmosphere is N2?

A

79%
- unavailable for use by most organism

127
Q

Know nitrogen cycling diagram

A

w3 content

128
Q

How do most bacteria divide?

A
  • binary fission, parent cell increases in size/cell volume and biomass then splits to two equal daughter cells
  • population doubles at each division
129
Q

How do bacteria divide asymmetrically?

A
  • 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
Q

What is generation (doubling) time?

A
  • the time it takes for a population to double
131
Q

What are some environmental conditions?

A
  • pH, temperature, competition with other organisms, nutrient supply
132
Q

What are some physical conditions?

A

gut pH, pH of infected fruit -> acidic

133
Q

How can we calculate binary fission?

A

Nt = N0 x 2n
Nt= final cell number
N0= original cell number
n= number of generation

134
Q

What is a fast and slow generation time?

A

Clostridium perfringens; ~10 minute
typically 20 mins
Mycobacterium leprae (causes leprosy); ~14 days

135
Q

When do bacteria divide at a constant interval?

A

unlimited & appropriate resources and environmental conditions

136
Q

What are some basics about microbial growth?

A
  • 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
Q

Explain how some prokaryotes are uncultured and why

A
  • 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
Q

What are the two main forms of culture media?

A
  • liquid media/broth (cells in suspension)
  • solid media (gelled/solidified with agar)
139
Q

What are some applications of liquid media/broth?

A
  • studying the growth characteristics of a pure culture; obtaining large numbers of cells &/or their extracellularly secreted products
140
Q

What are CFU?

A
  • 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
Q

What are the applications of solid media?

A
  • 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
Q

Name the types of microbial culture media?

A
  • complex/rich media
  • minimal defined media
  • enriched media
  • selective media
  • differential media
143
Q

Describe complex/rich media

A
  • nutrient rich; exact composition is poorly defined
  • ex: contain general extracts of yeast cell, plant and animal tissues
143
Q

Describe selective media

A
  • favour the growth of one organism over another
  • ex: high or low pH, plus antimicrobials, specific nutrients
144
Q

Describe minimal defined media

A
  • contain only those nutrients essential for a given microbe’s growth
  • exact components, known concentrations
145
Q

Describe enriched media

A
  • 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
Q

Describe differential media

A
  • 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
Q

What is the objective and our assumption of dilution streaking and spread plating to isolate of pure cultures?

A

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
Q

What is MacConkey media?

A
  • 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
Q

What are two techniques to isolate pure culture?

A
  • dilution streaking
  • spread plating
148
Q

Describe the process of dilution streaking

A
  • 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
Q

What is the result of dilution streaking?

A
  • 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
Q

What is the goal of diluting spread plates?

A
  • 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
Q

How do spread plates work for dilutions?

A
  • 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
Q

Why do we care to count microbes?

A
  • Government regulations for food industry, food
    handling facilities, health applications, etc.
  • Quality control (water safety; contamination;
    soil health; etc.)
  • Research
152
Q

How can we count microbes?

A
  • 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
Q

Describe Neubauer’s Chamber of Haemocytometer

A
  • 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
Q

Describe optical density

A
  • 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
Q

What is the microbial growth cycle?

A
  • 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
Q

What are the four phases of growth in the microbial growth cycle?

A

lag, exponential/logarithmic (log), stationary, death

155
Q

Briefly describe the lag phase of the microbial growth cycle

A
  • 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
Q

Briefly describe the exponential/logarithmic (log) phase of the microbial growth cycle

A
  • 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
Q

Briefly describe the stationary phase of the microbial growth cycle

A
  • 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
Q

What are planktonic cells?

A
  • single cells in suspension
  • swarmers: leave to colonize another area
159
Q

What are the two phases of the Exponential/logarithmic (log) phase?

A
  • 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
Q

Briefly describe the death phase of the microbial growth cycle

A
  • 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
Q

What does a chemostat ensure?

A
  • continuous logarithmic growth by constantly adding and removing equal amounts of culture medium
  • allows growth and growth conditions/environment to be highly controlled
162
Q

Describe feed/effluent for continous culture systems

A
  • feed and effluent inserted at same rate
  • constant nutrient accumulation, minimizes waste
  • bacteria are mostly happy entire time, can improve/maintain growth rate
163
Q

How could we classify bacteria?

A
  • shapes and arrangement
  • how they aggregate together
164
Q

What are some features of a “typica;” prokaryotic cell?

A
  • 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
Q

What are pili?

A
  • 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
Q

What are sex pili?

A
  • aka conjugation pili
  • type of pili
  • long, hollow, filamentous extensions from cell surface
167
Q

What are fimbriae?

A
  • shorter versions of pili (also hollow, shorter tubes)
  • used for adhesion (pathogens adhere to host cells and initiate disease)
168
Q

What are stalks?

A
  • 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
Q

What are flagella?

A
  • 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
Q

What are the different arrangements for flagella and describe them?

A
  • 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
Q

What is prokaryotic genetic material made of?

A
  • 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
Q

Desscribe genomes (prokaryotes) as prokaryotic genetic material

A
  • 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
Q

Describe plasmids as prokaryotic genetic material

A
  • 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
Q

What is Horizontal gene transfer (HGT)?

A
  • the transfer of genes between organisms, outside of traditional reproduction
  • Occurs almost exclusively in prokaryotes
  • replicates in straight line
174
Q

What is vertical gene transfer?

A
  • the transmission of genes from the parental generation to the offspring by asexual reproduction (binary fission)
  • meiosis
175
Q

What are some mechanisms of genetic diversification?

A

Transformation, transduction, conjugation
- asexual bacteria transfer
- do not sexually reproduce like meiosis cross over (recombination)

175
Q

Describe transformation as a mechanism of genetic diversification

A
  • allows cells to uptake DNA from environment
  • can acquire antimicrobial resistance
    fragmented: can enter another cell’s genome
  • takes up anything present
176
Q

Describe transduction as a mechanism of genetic diversification

A
  • 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
Q

Describe conjugation as a mechanism of genetic diversification

A
  • 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
Q

What are transposons, referenced to conjugation as a mechanism of genetic diversification?

A
  • 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
Q

Briefly describe the fluid mosaic model

A
  • 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
Q

Briefly describe the features of the fluid mosaic model

A

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
Q

Describe phospholipids in the fluid mosaic model

A
  • anchored in membrane; bound to protein
  • amphipathic molecules
  • Polar/charged (hydrophilic) head orient towards
    aqueous environment
  • Hydrophobic tails orient away from water
181
Q

Describe unsaturated fatty acid chains

A
  • melt at lower temp
  • increase fluidity; saturated lipids compress at low temp, press together, making a dense and rigid membrane
181
Q

Describe saturated fatty acid chains

A
  • melt at high temperatures
  • increase order/rigidity
181
Q

How are membrane lipids diverse from different cells?

A
  • 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
Q

What are sterols?

A
  • 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
Q

What are hopanoids/hopanes?

A
  • similar to sterols in eukaryotic membranes
  • carries out the same function as sterols but in bacteria
182
Q

How do prokaryotes regulate membrane fluidity and rigidity?

A
  • varying the abundance of these different membrane lipids and hopanoids
183
Q

How do archeal lipid tails differ?

A
  • kong isoprene chains with a methyl sidechain every 4 carbons
  • Bacteria: straight chains of fatty acid without branches
183
Q

What are the bonds that joinds the lipid tail to the glycerol?

A

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
Q

Describe a monolayer membrane in some archaea

A
  • Tails of two phospholipids fused into a single molecule with two polar heads
  • may make membranes more rigid to resist harsh environments
183
Q

What is the mirror image (enantiomer) of bacteria?

A
  • stereochemistry of archaeal glycerol moiety
184
Q

Explain the permeability barrier in prokaryotes

A
  • 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
Q

What does the Prokaryotic Cytoplasmic membrane serve as?

A
  • 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
Q

What are the 3 types of additional envelope layers in most bacteria?

A
  • 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
Q

What are most bacterial cell walls (sacculus) made of?

A
  • 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
Q

What does N-acetylmuramic acid bond to?

A
  • short peptide (4-6 amino acids)
185
Q

How do peptides cross-link?

A
  • via bond between D-Alanine and m-Diaminopimelic acid
  • connecting the parallel glycan strands
186
Q

How does vancomycin and penicillin work in trans-peptidase?

A
  • 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
Q

What does peptidoglycan help with?

A
  • confer cell shape
    Peptidoglycan
  • withstand turgor pressure (osmotic pressure arising from the cytoplasm and pressing against the cytoplasmic membrane; plants)
187
Q

How is peptidoglycan unique to bacteria relative to 2 antibiotics?

A

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
Q

How does peptidoglycan vary in gram-positive bacteria?

A
  • short (tetra)peptides of peptidoglycan chains
  • linked by bridges of pentapeptides made of glycines (pentaglycines)
  • multiple layers of peptidolgycan
189
Q

What is peptidoglycan threaded with in gram-positive bacteria?

A
  • 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
Q

What are the pros of gram-positive bacteria?

A
  • strong: very thick cell wall with lipoteichoic acids and teichoic acids thread through it adding strength
  • Protection against osmotic lysis
  • Gram-stain purple
190
Q

What are the cons of gram-positive bacteria?

A
  • Susceptible to lysozyme and other things that attack the cell wall, which is readily accessible
  • More susceptible to antibiotics than Gram-negative bacteria
191
Q

Describe the membranes in gram negative bacteria

A
  • 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
Q

What is LPS (lipopolysaccharide) in gram negative bacteria?

A
  • 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
Q

Describe LPS and serotyping in gram-negative bacteria

A
  • 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
Q

Describe serotyping; what does O and H mean of ex: E. coli O157:H7

A

O- specific O antigen for LPS
H- what antigens are present on the flagella

195
Q

What are the pros of gram negative bacteria?

A
  • 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
Q

What are the cons of gram negative bacteria?

A
  • 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
Q

What are some distinguishing characteristics of the mycobacterial cell wall?

A
  • 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
Q

Describe the mycobacteria envelope structure (mycomembrane)

A
  • 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
Q

What are the pros of mycobacteria?

A
  • 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
Q

What are the cons of mycobacteria?

A
  • grows slowly
  • cell envelope is energetically expensive to synthesize and maintain thick cell wall
200
Q

What is an S (surface)-layer?

A
  • 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
Q

What are some diverse functions of the surface-layer in the prokaryotic cell wall?

A
  • 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
Q

Describe the archaeal cell wall

A
  • 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
Q

Describe the proteinaceous S-layer in archaeal cell walls

A
  • 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
Q

Describe pseudomurein in archaeal cell walls

A

pseudopeptidoglycan
- a few species
- with N-acetylalosaminuronic acid (NAT) rather than NAM; forms stronger peptide interbridges

203
Q

Describe methanochondroitin in archaeal cell walls

A
  • 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
Q

What are the functions of the prokaryotic cell wall?

A

● Protection against the immune system; prevent phagocytosis (encapsulated is dangerous)
● Assist with adherence
● Protection from dehydration

205
Q

Describe capsules on the prokaryotic cell wall

A
  • 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
Q

Describe phylum cyanobacteria

A
  • 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
Q

Describe bacterial diversity

A
  • 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
Q

Name the best studied phyla of domain bacteria

A
  • Oxygenic phototrophs: Cyanobacteria
  • Gram-positive: Firmicutes & Actinobacteria
  • Gram-negative: Proteobacteria
  • Gram-negative: Spirochetes, Bacteroidetes
  • PVC Superphylum: Planctomycetes, Verrucomicrobia, and Chlamydiae
207
Q

Describe encapsulate forms of capsules

A
  • 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
Q

What are CO2-fixing enzymes?

A
  • very specific
  • function within Calvin cycle
  • ex: rubisco
208
Q

What are specialized protein microcompartments?

A

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
Q

What are thylakoids?

A
  • 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
Q

What is Prochloroccus marinus?

A
  • Marine cyanobacteria; one of the most plentiful organisms on Earth
  • Responsible for production of ~20% of oceanic photosynthesis!
209
Q

Describe gas vesicles as a specialized structure

A
  • allows microbes to float; aquatic phototrophs and some aquatic heterotrophs
  • typically aqueous, in water environments
210
Q

What are specialized structures?

A
  • specialized within bacteira, polyhedral, permeable (molecules go in/out), made of rubisco, enzyme in very high conc.
211
Q

What is cyanobacterium Microcystis?

A
  • 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
Q

Describe the implications of toxic microcystic algal

A
  • 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
Q

What is the cyanobacterial cell structure, and how do specialized structures affect it?

A
  • 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
Q

Which cyanobacteria are toxic?

A
  • 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
Q

Describe some real life versions of cyanobacteria?

A

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
Q

How can we classify microorganisms based on environmental conditions?

A

temperature, pH, osmolarity, oxygen, pressure

215
Q

**What are facultative anaerobes?

A

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
Q

**What are aerotolerant anaerobes?

A
  • 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
Q

**Describe microaerophiles

A
  • must use oxygen to generate energy, but high concentration of it kills them
  • can’t ferment or in anaerobic condition
215
Q

Describe aerobic and anaerobic respiration

A
  • 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
Q

What is fermentation?

A
  • glycolysis generates ATP
216
Q

What are barophiles?

A
  • organisms under high pressure
217
Q

What are superphylum proteobacteria?

A
  • 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
Q

What are the possible diverse metabolisms of superphylum proteobacteria?

A
  • fermentation
  • aerobic & anaerobic respiration: heterotrophs, photoheterotrophs
219
Q

What are the possible diverse lifestyles of superphylum proteobacteria?

A
  • single free-living in various habitats
  • in symbiosis with plants and animals
  • some are pathogens
  • plats into dif. symbiotic relationships
220
Q

What are phylum alphaproteobacteria?

A
  • 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
Q

What are phylum gammaproteobacteria?

A
  • 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
Q

What are phylum gammaproteobacteria?

A
  • 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
Q

What are the distinct phylogenetic branches of gram positive bacteria?

A
  • phylum firmicutes (thick peptidoglycan; low-GC species)
  • phylum actinobacteria (high-GC species)
223
Q

Describe phylum firmicutes in the genus bacillus

A
  • 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
Q

Describe phylum firmicutes in the genus clostridium

A
  • 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
Q

What are some non-spore-forming firmicutes?

A
  • staphylococcus
  • streptococcus
    within soil and other areas of nature
226
Q

Describe staphylococcus

A
  • Facultative anaerobes
  • Cocci in clusters
  • Staphylococcus aureus (S. aureus)
    § Methillicin-resistant Staphylococcus aureus (MRSA)
226
Q

Describe streptococcus

A
  • Aerotolerant
  • Cocci in chains
  • Streptococcus pneumoniae
  • S. pyogenes
227
Q

What is phylogeny based on?

A

both the small subunit 16S rRNA and genome sequences

227
Q

What is the phylogeny of domain archaea?

A
  • 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
Q

What does polyphyletic mean?

A
  • ancestor not in group
228
Q

What are methanogens?

A
  • 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
Q

What are the environmental niches of euryarchaeota methanogens?

A

-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
Q

What do methanogens cause?

A
  • 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
Q

What is global warming doing to permafrost?

A
  • 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
Q

Describe thermophiles

A
  • 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
Q

Describe the structure of methanogens

A
  • archaea: rigid cell walls made of pseudopeptidoglycan, sulfated polysaccharides or proteins; S layer
  • morphologically diverse
  • rods (single or filamentous), cocci, spirals
232
Q

Give an example of a hyperthermophile

A
  • 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
Q

How have we used archaea in biotechnology?

A
  • 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

YR2SEM1 (10 decks)

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