Chapter 1 – Microorganisms and microbiology
Prokaryote Eukaryote
No nucleus Nucleus
Free DNA in cytoplasm DNA in nucleus
No mitochondria Mitochondria
ATP generated in cell membrane ATP generated through oxidative phosphorylation
Transcription and translation in cytoplasm Transcription in nucleus and translation in cytoplasm
Complex cell wall (peptidoglycan) No or simple cell wall
70S ribosomes (50S + 30S) 80S ribosomes (60S + 40S)
Differences archaea with bacteria:
- A way of coiling/packaging of the chromosomes that resemble that of eukaryotes
- Different composition of the cell wall and cell membrane (no peptidoglycan and different types of lipids)
! O2 uit photosynthese komt van de H2O!
Microorganisms constitute the majority of the biomass on earth and have created the environmental conditions
as they are now > physically and chemically (e.g. oxygen production and closing the biochemical cycles)
Carl Woese (1928-2012) was a physicist who discovered the archaea as a separate group of prokaryotes, based
on rRNA sequences. He got a lot of criticism from biologists.
rRNA sequences are now used for taxonomy of microorganisms (phylogenetic tree) and the microbial diversity
of ecosystems:
- rRNA is present in all life forms
- rRNA has the same function in every organism
- rRNA is very conserved (changes little over time by mutations)
- rRNA sequences are long enough
Habitat – environment in which a microbial population lives
Microbial communities – where microbial populations interact with other populations
Ecosystem – all the living organisms together with the physical and chemical components of their environment
,Clostridium botulinum – toxic microorganisms which lives in oxygen-poor water. 70 μg of the microorganism can
kill a human (type H: 2 ng is lethal). Same toxin is also in botox, but much more diluted.
Yersinia pestis – microorganism which is transferred from rats to humans by fleas. It caused the Black death
between 1347-1351.
Alexander Fleming (1881-1955) discovered penicillin by accidence in 1929 (actually penicillin was already
discovered in 1896 by Duchesne, but he never published it).
Antimicrobial agents naturally produced by microorganisms. They have the ability to either kill or inhibit the
growth of bacteria. But microorganism have certain resistance mechanisms:
Advantages of bacteria:
- Soil: N2 + 8H -> 2NH3 + H2 (only bacteria can fixate nitrogen)
- Cows: Grass > cellulose > glucose > microbial fermentation > fatty acids (in milk, cheese etc.) + CO2 + CH4
- Food
- Production of low- and high value products (antibiotics, enzymes, chemicals)
- Production of biofuels (methane, ethanol, butanol)
- Wastewater treatment
- Bioremediation: cleaning up pollutants
Light microscopy (bright-field microscopy: cells have little contrast)
Improve contrast by:
- Staining (methylene blue, cristal violet, safranin) > cells die
- Differential staining (Gram- stain) > cells die
- Phase contrast (phase-difference amplified)
- Dark field (light from the side, not passing the specimen)
- Fluorescence (naturally (chlorophyll) or stained (DAPI))
,Electron microscopy (two types):
- Transmission electron microscopes (TEM)
- Scanning electron microscopes (SEM)
Antonie van Leeuwenhoek (1632-1723) created (lenses for) microscopes and was the first to observe
microorganisms.
Louis Pasteur (1822-1895) discovered the pasteurisation/sterilisation process (no entrance from contaminated
air, no bacteria). He also discovered that alcoholic fermentation was a biologically (not just chemically) mediated
process. He discovered that some microorganisms (bacteria and moulds) can grow with oxygen and others can
grow without.
Aerobic organisms – organisms which respire with O2, which is the electron acceptor. The oxygen is used to
‘burn’ a compound, and the compound becomes oxidized. Electrons are released from the substrate, which is the
electron donor. Electrons pass via a respiratory chain to the terminal electron acceptor, O2, and the respiration
leads to energy generation in the form of ATP.
Anaerobic organisms – respire with another electron acceptor (e.g NO3-, SO42-, CO2, Fe3+, Mn4+ etc.) or they are
fermentative, meaning that they do not respire, but use an internal metabolite as electron acceptor (e.g. yeasts).
3 ways to lose electrons:
- Aerobic respiration – glucose (oxidized, so e- released, during glycolysis) > pyruvate (more e- released) >
CO2. O2 acts as electron acceptor and is turned into H2O
- Anaerobic respiration – NO3- > N2
- Fermentation – pyruvate can also act as its ‘own’ electron acceptor and becomes lactate, glucose is
converted into ethanol when it releases e-
Martinus Beijerinck (1851-1931) discovered the microbial diversity. By creating different conditions, you can
grow certain microorganisms. He was also the first to describe viruses.
Virus:
- protein shell with DNA or RNA in it
- No ribosomes present, so it cannot make proteins by itself: it needs host cells to multiply
- Uses the RNA/DNA replication and protein synthesis machinery of the host
- Have their own taxonomy: morphology, type nucleic acid, host
- Much smaller than yeast cells or bacterial cells
Sergei Winogradsky (1856-1953) discovered
microorganisms that can oxidize iron, sulfur, ammonium etc
and discovered that energy (ATP) was generated from
reduced compounds. He proposed the concept of
chemolithoautotrophy (inorganic molecules serve as
electron donor for respiration, C from CO2 is used)
, Chapter 2 – Microbial cell structure and function
Major morphologies (cell shapes) of prokaryotic cells:
Sometimes selective forces may affect morphology:
- Optimization for nutrient uptake or energy conservation
- Swimming motility (helical or spiral-shaped cells)
- Gliding motility (filamentous cells)
Pleomorphism – ability of some microorganisms to alter their
shape or size in response to environmental conditions
Swarmer cells are not able to divide on their own. They first
have to attach to a surface, after which a new swarmer cell can be produced (little phosphate > stalk is long, lot
of phosphate > stalk is short)
Beggiatoa – chemolithotrophic bacteria which make long filaments on the interface between different
environmental conditions, in this case the interface between electron donor and electron acceptor, which
transfer the electrons.
Epulopiscium fishelsoni – live in the GI tract of certain fish. They are polyploid, some with over 100.000 genome
copies per cell. To overcome the size limitations, it has many folds in the cell wall and many transport proteins
located in the membrane.
Proteins (55%) and rRNA (20%) make up the most of the dry weight of a prokaryotic cell.
Being small has many advantages to prokaryotes:
- More surface area relative to cell volume than large cells
- Support greater nutrient and waste product exchange per unit cell volume
- Tend to grow faster than larger cells
Mycoplasma pneumoniae is the most abundant, and probably (one of) the smallest organism(s) in the oceans
(about 25% of all microbial cells)
Functions of the cell membrane:
- Surrounds cytoplasm
- Separates it from the environment
- Main function: selective permeability (nutrients transported in and waste products out)
Integral membrane proteins are significantly embedded in the cell, peripheral membrane proteins are loosely
attached and located at the outside or inside.
Prokaryote Eukaryote
No nucleus Nucleus
Free DNA in cytoplasm DNA in nucleus
No mitochondria Mitochondria
ATP generated in cell membrane ATP generated through oxidative phosphorylation
Transcription and translation in cytoplasm Transcription in nucleus and translation in cytoplasm
Complex cell wall (peptidoglycan) No or simple cell wall
70S ribosomes (50S + 30S) 80S ribosomes (60S + 40S)
Differences archaea with bacteria:
- A way of coiling/packaging of the chromosomes that resemble that of eukaryotes
- Different composition of the cell wall and cell membrane (no peptidoglycan and different types of lipids)
! O2 uit photosynthese komt van de H2O!
Microorganisms constitute the majority of the biomass on earth and have created the environmental conditions
as they are now > physically and chemically (e.g. oxygen production and closing the biochemical cycles)
Carl Woese (1928-2012) was a physicist who discovered the archaea as a separate group of prokaryotes, based
on rRNA sequences. He got a lot of criticism from biologists.
rRNA sequences are now used for taxonomy of microorganisms (phylogenetic tree) and the microbial diversity
of ecosystems:
- rRNA is present in all life forms
- rRNA has the same function in every organism
- rRNA is very conserved (changes little over time by mutations)
- rRNA sequences are long enough
Habitat – environment in which a microbial population lives
Microbial communities – where microbial populations interact with other populations
Ecosystem – all the living organisms together with the physical and chemical components of their environment
,Clostridium botulinum – toxic microorganisms which lives in oxygen-poor water. 70 μg of the microorganism can
kill a human (type H: 2 ng is lethal). Same toxin is also in botox, but much more diluted.
Yersinia pestis – microorganism which is transferred from rats to humans by fleas. It caused the Black death
between 1347-1351.
Alexander Fleming (1881-1955) discovered penicillin by accidence in 1929 (actually penicillin was already
discovered in 1896 by Duchesne, but he never published it).
Antimicrobial agents naturally produced by microorganisms. They have the ability to either kill or inhibit the
growth of bacteria. But microorganism have certain resistance mechanisms:
Advantages of bacteria:
- Soil: N2 + 8H -> 2NH3 + H2 (only bacteria can fixate nitrogen)
- Cows: Grass > cellulose > glucose > microbial fermentation > fatty acids (in milk, cheese etc.) + CO2 + CH4
- Food
- Production of low- and high value products (antibiotics, enzymes, chemicals)
- Production of biofuels (methane, ethanol, butanol)
- Wastewater treatment
- Bioremediation: cleaning up pollutants
Light microscopy (bright-field microscopy: cells have little contrast)
Improve contrast by:
- Staining (methylene blue, cristal violet, safranin) > cells die
- Differential staining (Gram- stain) > cells die
- Phase contrast (phase-difference amplified)
- Dark field (light from the side, not passing the specimen)
- Fluorescence (naturally (chlorophyll) or stained (DAPI))
,Electron microscopy (two types):
- Transmission electron microscopes (TEM)
- Scanning electron microscopes (SEM)
Antonie van Leeuwenhoek (1632-1723) created (lenses for) microscopes and was the first to observe
microorganisms.
Louis Pasteur (1822-1895) discovered the pasteurisation/sterilisation process (no entrance from contaminated
air, no bacteria). He also discovered that alcoholic fermentation was a biologically (not just chemically) mediated
process. He discovered that some microorganisms (bacteria and moulds) can grow with oxygen and others can
grow without.
Aerobic organisms – organisms which respire with O2, which is the electron acceptor. The oxygen is used to
‘burn’ a compound, and the compound becomes oxidized. Electrons are released from the substrate, which is the
electron donor. Electrons pass via a respiratory chain to the terminal electron acceptor, O2, and the respiration
leads to energy generation in the form of ATP.
Anaerobic organisms – respire with another electron acceptor (e.g NO3-, SO42-, CO2, Fe3+, Mn4+ etc.) or they are
fermentative, meaning that they do not respire, but use an internal metabolite as electron acceptor (e.g. yeasts).
3 ways to lose electrons:
- Aerobic respiration – glucose (oxidized, so e- released, during glycolysis) > pyruvate (more e- released) >
CO2. O2 acts as electron acceptor and is turned into H2O
- Anaerobic respiration – NO3- > N2
- Fermentation – pyruvate can also act as its ‘own’ electron acceptor and becomes lactate, glucose is
converted into ethanol when it releases e-
Martinus Beijerinck (1851-1931) discovered the microbial diversity. By creating different conditions, you can
grow certain microorganisms. He was also the first to describe viruses.
Virus:
- protein shell with DNA or RNA in it
- No ribosomes present, so it cannot make proteins by itself: it needs host cells to multiply
- Uses the RNA/DNA replication and protein synthesis machinery of the host
- Have their own taxonomy: morphology, type nucleic acid, host
- Much smaller than yeast cells or bacterial cells
Sergei Winogradsky (1856-1953) discovered
microorganisms that can oxidize iron, sulfur, ammonium etc
and discovered that energy (ATP) was generated from
reduced compounds. He proposed the concept of
chemolithoautotrophy (inorganic molecules serve as
electron donor for respiration, C from CO2 is used)
, Chapter 2 – Microbial cell structure and function
Major morphologies (cell shapes) of prokaryotic cells:
Sometimes selective forces may affect morphology:
- Optimization for nutrient uptake or energy conservation
- Swimming motility (helical or spiral-shaped cells)
- Gliding motility (filamentous cells)
Pleomorphism – ability of some microorganisms to alter their
shape or size in response to environmental conditions
Swarmer cells are not able to divide on their own. They first
have to attach to a surface, after which a new swarmer cell can be produced (little phosphate > stalk is long, lot
of phosphate > stalk is short)
Beggiatoa – chemolithotrophic bacteria which make long filaments on the interface between different
environmental conditions, in this case the interface between electron donor and electron acceptor, which
transfer the electrons.
Epulopiscium fishelsoni – live in the GI tract of certain fish. They are polyploid, some with over 100.000 genome
copies per cell. To overcome the size limitations, it has many folds in the cell wall and many transport proteins
located in the membrane.
Proteins (55%) and rRNA (20%) make up the most of the dry weight of a prokaryotic cell.
Being small has many advantages to prokaryotes:
- More surface area relative to cell volume than large cells
- Support greater nutrient and waste product exchange per unit cell volume
- Tend to grow faster than larger cells
Mycoplasma pneumoniae is the most abundant, and probably (one of) the smallest organism(s) in the oceans
(about 25% of all microbial cells)
Functions of the cell membrane:
- Surrounds cytoplasm
- Separates it from the environment
- Main function: selective permeability (nutrients transported in and waste products out)
Integral membrane proteins are significantly embedded in the cell, peripheral membrane proteins are loosely
attached and located at the outside or inside.
