Samenvatting
Samenvatting Microbiology
Dit is een samenvatting van het vak microbiology gegeven door professor Rineau. Ik was geslaagd in eerste zit door de powerpoints en deze samenvatting te leren, het handboek is niet noodzakelijk.
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Voorbeeld 6 van de 57 pagina's
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Samenvatting MicrobiologyInhoudsopgave
HC1: introductie ......................................................................................................................................................................... 4
Relevance of microbes .................................................................................................................................................................... 4
Cells ................................................................................................................................................................................................ 4
Ecology ........................................................................................................................................................................................... 4
Evolution......................................................................................................................................................................................... 5
Impact on humans.......................................................................................................................................................................... 5
History of microbiology .................................................................................................................................................................. 5
HC2: Microbial cell structure ...................................................................................................................................................... 6
Cell morphology and size................................................................................................................................................................ 6
The cytoplasmic membrane ........................................................................................................................................................... 6
Prokaryotic cell wall ....................................................................................................................................................................... 7
The outer membrane ...................................................................................................................................................................... 8
Cell walls of Archaea ...................................................................................................................................................................... 9
Cell surface structures and inclusions ............................................................................................................................................. 9
Microbial locomotion (=bewegen) ............................................................................................................................................ 11
Flagella and swimming ................................................................................................................................................................ 11
Gliding .......................................................................................................................................................................................... 12
Taxis .............................................................................................................................................................................................. 13
HC3 + 4 + 5: Microbial growth................................................................................................................................................... 14
Bacterial Cell Division ................................................................................................................................................................... 14
Cell Growth and Binary Fission ................................................................................................................................................ 14
Fts Proteins and Cell Division .................................................................................................................................................. 14
MreB and Determinants of Cell Morphology .......................................................................................................................... 14
Population Growth ....................................................................................................................................................................... 15
The Concept of Exponential Growth ....................................................................................................................................... 15
The Mathematics of Exponential Growth ................................................................................................................................ 15
The Microbial Growth Cycle .................................................................................................................................................... 15
Continuous Culture: The Chemostat ....................................................................................................................................... 15
Measuring Microbial Growth ....................................................................................................................................................... 16
Microscopic Counts ................................................................................................................................................................. 16
Viable Counts........................................................................................................................................................................... 16
Turbidimetric Methods ............................................................................................................................................................ 16
Temperature and Microbial Growth ............................................................................................................................................. 17
Effect of Temperature on Growth ............................................................................................................................................ 17
Microbial Life in the Cold ......................................................................................................................................................... 17
Microbial Life at High Temperatures ....................................................................................................................................... 17
Other Environmental Factors Affecting Growth ........................................................................................................................... 18
Acidity and Alkalinity ............................................................................................................................................................... 18
Osmotic Effects on Microbial Growth ...................................................................................................................................... 18
Oxygen and Microorganisms ................................................................................................................................................... 18
Toxic Forms of Oxygen ............................................................................................................................................................. 18
Nutrition and culture of microorganisms ..................................................................................................................................... 19
, Nutrition and Cell Chemistry ................................................................................................................................................... 19
Culture Media .......................................................................................................................................................................... 20
Laboratory Culture .................................................................................................................................................................. 20
HC6+7: Metabolism of microorganisms .................................................................................................................................... 21
Energetics and catalysis ............................................................................................................................................................... 21
Oxidoreduction ............................................................................................................................................................................. 21
Energy storage ............................................................................................................................................................................. 21
Metabolic diversity of microorganisms ........................................................................................................................................ 22
Aerobic respiration .................................................................................................................................................................. 22
Anaerobic respiration .............................................................................................................................................................. 22
Fermentation ........................................................................................................................................................................... 23
Chemolithotrophy ................................................................................................................................................................... 25
Phototrophy ............................................................................................................................................................................ 26
HC8: Diversity of bacteria ......................................................................................................................................................... 28
Proteobacteria.............................................................................................................................................................................. 28
Proteobacteria (α) ................................................................................................................................................................... 28
Proteobacteria (β) ................................................................................................................................................................... 28
Proteobacteria (γ) .................................................................................................................................................................... 29
Proteobacteria (δ) ................................................................................................................................................................... 29
Proteobacteria (ε) .................................................................................................................................................................... 29
Firmicutes ..................................................................................................................................................................................... 30
Actinobacteria ......................................................................................................................................................................... 31
Bacteroidetes ............................................................................................................................................................................... 31
Tenericutes ................................................................................................................................................................................... 32
Chlamydiae ................................................................................................................................................................................... 32
Planctomycetes ............................................................................................................................................................................ 32
Verrucomicrobia ........................................................................................................................................................................... 32
Thermotogae ................................................................................................................................................................................ 32
Aquificae....................................................................................................................................................................................... 33
Deinococci .................................................................................................................................................................................... 33
Spirochaetes ................................................................................................................................................................................. 33
Anderen ........................................................................................................................................................................................ 33
HC9: Major Microbial Habitats and Diversity ............................................................................................................................ 34
Microbial Ecology ......................................................................................................................................................................... 34
General Ecological Concepts.................................................................................................................................................... 34
Ecosystem Service: Biogeochemistry and Nutrient Cycles ...................................................................................................... 34
The Microbial Environment .......................................................................................................................................................... 34
Environments and Microenvironments ................................................................................................................................... 34
Surfaces and Biofilms .............................................................................................................................................................. 35
Microbial Mats ........................................................................................................................................................................ 36
Terrestrial Environments............................................................................................................................................................... 36
Soils ......................................................................................................................................................................................... 36
The Subsurface ........................................................................................................................................................................ 36
Aquatic Environments .................................................................................................................................................................. 36
Freshwaters ............................................................................................................................................................................. 36
Coastal and Ocean Waters: Phototrophic Microorganisms ..................................................................................................... 37
Pelagic Bacteria, Archaea, and Viruses ................................................................................................................................... 37
Terrestrial VS aquatic ............................................................................................................................................................... 37
The Deep Sea and Deep-Sea Sediments .................................................................................................................................. 37
Hydrothermal Vents ................................................................................................................................................................ 38
,HC10: Nutrient Cycles, Biodegradation, and Bioremediation .................................................................................................... 39
Nutrient Cycles ............................................................................................................................................................................. 39
The Carbon Cycle ..................................................................................................................................................................... 39
Syntrophy and Methanogenesis .............................................................................................................................................. 39
The Nitrogen Cycle .................................................................................................................................................................. 39
The Sulfur Cycle ....................................................................................................................................................................... 39
The Iron Cycle .......................................................................................................................................................................... 39
Microbial Symbioses ................................................................................................................................................................. 39
Plants as Microbial Habitats ........................................................................................................................................................ 39
The Legume–Root Nodule Symbiosis ...................................................................................................................................... 39
Agrobacterium and Crown Gall Disease .................................................................................................................................. 40
Mammals as Microbial Habitats .................................................................................................................................................. 41
The Rumen and Ruminant Animals ......................................................................................................................................... 41
Insects as Microbial Habitats ....................................................................................................................................................... 42
Heritable Symbionts of Insects ................................................................................................................................................ 42
Termites ................................................................................................................................................................................... 43
Aquatic Invertebrates as Microbial Habitats ................................................................................................................................ 43
Hawaiian Bobtail Squid ............................................................................................................................................................ 43
Marine Invertebrates at Hydrothermal Vents and Gas Seeps ................................................................................................. 44
HC11: Viruses ........................................................................................................................................................................... 45
Virus types .................................................................................................................................................................................... 45
Structure of viruses ....................................................................................................................................................................... 45
Ecology ......................................................................................................................................................................................... 46
Human virome .............................................................................................................................................................................. 48
Viroids and prions......................................................................................................................................................................... 49
HC12 + 13: Microbial diseases .................................................................................................................................................. 51
Principles of epidemiology ........................................................................................................................................................... 51
Person-to-person diseases (25) .................................................................................................................................................... 51
Vectorborne diseases.................................................................................................................................................................... 52
Soilborne diseases ........................................................................................................................................................................ 52
Waterborne diseases .................................................................................................................................................................... 52
Foodborne diseases ...................................................................................................................................................................... 52
HC14: Microbes in industry ...................................................................................................................................................... 53
Bioleaching ................................................................................................................................................................................... 53
Bioremediation ............................................................................................................................................................................. 53
Wastewater treatment ................................................................................................................................................................. 54
Other ............................................................................................................................................................................................ 56
,HC1: introductie
Relevance of microbes
Microbe = onzichtbaar voor het blote oog ➔ Bacteriën, virussen, gisten, protisten & fungi
• Groeit snel & is makkelijk te manipuleren ➔ goede modellen
o Medicijnen, voedsel, industrie, biochemie…
• Kunnen leven in meest extreme condities
Cells
• Kolonies hebben verschillende densiteiten met miljoenen prokaryote cellen
• Veel microben morfologisch gelijk, maar metabolisch zeer verschillend
Opbouw prokaryoot VS eukaryoot:
• Prokaryoot: bacteriën & archea
• Eukaryoot: fungi, gist, protisten & algen
• Genoom bepaald de mogelijkheid tot adaptatie
o Circulair chromosoom/plasmiden/…
o Virussen < prokaryoten < eukaryoten
o Hangt ook af van levensstijl ➔ als ze een host nodig hebben
is het genoom kleiner
o Door genetische uitwisseling evolueren microben snel
(resistentie opbouwen)
o Adaptatie naar
▪ Bewegen (flagellen)
▪ Differentiatie (sporen)
▪ Communicatie
Ecology
Ecosysteem = alle levende organismes + chemische & fysische aspecten
• Voorbeeld: gletsjer
Invloed van de omgeving op microben:
• pH
• Nutriënten
• Temperatuur
• Vochtigheid
• O2
• Druk
Invloed van microben op omgeving:
• Bacterial blooms (bv: cyanobacteriën) (ze groeien zo snel dat ze zichtbaar worden en water
vertroebelen)
• Decompositie ➔ anders zaten we nu op meters hoog, dood materiaal
,Evolution
• Microben fossiliseren niet ➔ moeilijk te onderzoeken
• Aangepast aan alle mogelijke habitats, want tijd genoeg om te
adapteren
• Zitten vooral in aard-/oceaanbodems en oppervlaktes
Impact on humans
Kan voordelen/nadelen hebben (meer voordelige micro-organismen dan
nadelige)
• Menselijke ziektes veel door microben ➔ oplossing = antibiotica & vaccinatie
• Agricultuur
o +: stikstoffixerende bacteriën, cellulose afbraak in maag, regeneratie van nutriënten in
bodem & water
o -: ziektes in dieren & planten
• Voedsel
o +: fermentatie (yoghurt, kaas, bier, brood, …)
o -: vervallen ➔ schimmelen…
• Industrie
o Energie, antibiotica, ontmijnen, wastewater treatment, …
• Genetic engeneering
o Antibiotica, enzymen, chemicaliën, insuline, …
History of microbiology
• Ontstaan toen de microscoop werd uitgevonden (17e eeuw) & met die evolutie meegegaan
• Vruchtstructuren van schimmels en endosporen van bacteriën werden ontdekt
• Louis Pasteur heeft de theorie van spontane generatie weerlegd, microben verschijnen niet out of
the blue, en zijn dus te kweken en te controleren
• Pasteur’s swan-necked flask experiment:
• Koch’s Postulates (link tussen oorzaak en effect van de besmetting):
, HC2: Microbial cell structure
Cell morphology and size
Algemene vormen:
• Coccus (rond/ovaal)
• Rod (cylinder)
• Spirillum
Ongewone vormen:
• Spirochetes
• Appendaged (lijken op fungi hyfen, maar veel kleiner)
• Filamentous (heel lang)
Vorm is niet zo informatief ➔ wel voor voedingsopname en zwemmogelijkheden
Grootte:
• Prokaryoten: 0.5 – 4 µm
• Eukaryoten: 10 ➔ 200 µm
• Upper limit ➔ anders kan het metabolisme niet onderhouden worden
• Lower limit ➔ alle componenten moeten erin kunnen ➔ pathogenen kunnen wel kleiner
zijn aangezien die dingen kunnen krijgen van hun host
• Voordeel aan klein zijn: meer celoppervlakte tov volume ➔ hogere voedingsopname per
unit celvolume ➔ sneller groeien
The cytoplasmic membrane
Omschrijving:
• Cytoplasma scheiden van omgeving
• Doorlaatbaar maar selectief
o Concentratie van specifieke metabolieten bepalen
o Excretie van afvalproducten
• Opbouw:
o Fosfolipiden dubbellaag:
▪ Hydrofoob(vetzuren) + hydrofiel
o Eiwitten in membraan:
▪ Functie: substraat transport/energieopbrengst
o Membraanversterkers:
▪ Kationen binden aan – ladingen van fosfolipiden
▪ Planaire structuur zorgt voor stabiliteit
• Verschillen:
o Archea bevatten ether linken met fosfolipiden, isoprene staarten en bi-
/monolaag
o Esterbindingen zijn bacteriën of eukaryoten, net zoals vetzuurstaarten
en een bilaag
• Functie doorlaatbaarheid:
o Hoe kleiner, minder geladen en meer hydrofoob, hoe makkelijker het
erdoor kan gaan
o Transporters nodig:
▪ Tegen concentratigradient werken ➔ energie nodig
▪ Aquaporinen ➔ waterdiffusie
▪ Bidirectioneel transport
▪ …
o Verschillende types transport:
▪ Simpel transport: proton motive force (proton zoals
lactose bindt en activeert een conformatieverandering
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