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MIC2011

Intro to Microbiology - Theme 1

QuestionAnswer
microorganisms/microbe life form too small to be seen with the human eye
culture a collection of microbial cells that been grown in a nutrient medium
microbial growth increase in cell number due to replication
colony a visible mass of cultured microbial cell arising from a single cell
microbiome the community of microorganisms occupying a given well-defined habitat
prokaryotic microbes bacteria and archaea
eukaryotic microbes protists: fungi, slime molds, microscopic algae, protozoa
example of fungi yeasts, molds
example of protists algae, protozoa, slime molds
example of bacteria Escherichia coli
example of archaea methanogens
virus composition protein and nucleic acid
viroid composition RNA
satellites composition nucleic acid enclosed in a protein shell
prions composition proteins
light microscopes allows visualisation of bacteria, archaea, and some viruses. fluorescence light microscopy can give additional information 500nm to 10mm
electron microscopes required for most viruses, and for many prokaryotic cell structures
early earth hot and anoxic
first microbes anaerobes, get energy from inorganic molecules. early photosynthetic microbes were anoxygenic, purple sulfur bacteria and green sulfur bacteria
cyanobacteria transformed life on earth. increased oxygen. gave the possibility for aerobic life. decreased methane in atmosphere which reduces temperatures on Earth.
how were aerobic microbes and all eukaryotes formed? temperature became colder and increased oxygen killed many of the early microbes and created the conditions for new ones. allowed the evolution of aerobic (oxygen) microbes and all eukaryotes
visual research approaches microscopy-based, cell size, shape, structures
functional research approaches culture-based, metabolic capabilities, cell behaviour
genomic research approaches single gene/ whole genome comparisons. evolutionary relationships, predicted functions
why ribosomal RNA to show relatedness? present in all life forms, changes very slowly, possible to sequences in 1970s.
comparative genomics showing relatedness DNA replication, transcription, translation genes are more similar to Archaea. Mitochondrial and chloroplast genes are closer to bacteria. most metabolic genes are more similar to genes.
WEEK 1, PART 1 - SUMMARY 1. microbes are the dominant form of life on Earth 2. life on Earth likely began with anaerobic, thermophilic cells able to get energy from minerals 3. cyanobacteria let to evolution of all aerobic life by producing oxygen
WEEK 1, PART 1 - SUMMARY 2 4. our understanding of microbial diversity and evolution has increased with new research approaches 5. molecular methods support the division of today's life forms into three domains: - archaea - bacteria - eukarya Eukarya= hybrid of bact. and archaea
prokaryotic cell architecture cell wall, cytoplasmic membrane, cytoplasm, nucleoid, plasmid, ribosome
eukaryotic cell architecture cell wall, cytoplasmic membrane, mitochondrion, nuclear membrane, nucleus, ribosomes, ER, cytoplasm, golgi body
unifying features of microbes (UFOM) adaptation, cell size, cell structure, macromolecules, genomes, metabolism
adaptation (UFOM) all microbes are able to evolve to display new properties, mutation. microbes can also exchange DNA with other cells. haploid genomes and short generation times mean that adaptation can happen quickly
cell size (UFOM) cells need to exchange molecules. almost all microbes are small (<100 micrometres). some large microbes have ruffled, folded outer membrane to increase SA
cell structure (UFOM) cytoplasmic membrane. phospholipid bilayer. cell walls
macromolecules (UFOM) all cells share a common 'language of life' for info storage and processing. machinery to produce and convert between these molecules is also conserved.
genomes (UFOM) microbial cells' DNA genomes have compacted and organised by specific proteins. prokaryotic have circular chromosomes
metabolism (UFOM) all microbes can grow by producing chemical reaction = energy = ATP
not unifying features of microbes cell shape. prokaryotes (lack of organelles, lack of internal organisation/ structure). specific metabolic capabilities
morphologies of bacteria and archaea rods, cocci, spiral, square
example of rod shaped organism Shigella flexneri
example of cocci shaped organism Staphylococcus aureus
example of spiral shaped organism Borrelia burgdoferi
example of square shaped organism Haloquadratum
habitats of bacteria and archaea ocean, soil, humans, plants, extreme e.g. hydrothermal vents, salt lakes
microbial abilities common motility, chemical communication between cells, horizontal gene transfer. differentiation into specialised cell types e.g. spores
microbial abilities uncommon multicellularity, predation, extreme survival capabilities, magnetotaxis
bacteria 30-80 major phyla. present in all but the most extreme environments on Earth. incl. humans, plants and animal pathogen
archaea 5-12 phyla. present widely in nature and associated with human and animals. incl. most extremophiles. no known pathogens
a 'typical' prokaryote bacterial. 1-2 micrometres. circular genome. adapted to temperate conditions. free-living, not an obligate parasite/symbiont. heterophobic. present in low-nutrient conditions. embedded in a microbial community, possibly attached to a surface.
benefits of microbial community attached to a surface greater access to nutrients. protection from predation and physical disturbances. a means to stay in a hospitable environments. surfaces can be biological or abiotic
what do surface attached microbes often form? biofilms. offers protection. facilitates microbe to microbe interactions
WEEK 1, PART 2 - SUMMARY 1. unifying features of microbes include cell membranes, use of 3 macromolecules of life (DNA-RNA-protein), capacity for adaptation and growth, small size and metabolism that uses ATP.
WEEK 1, PART 2 - SUMMARY 2 2. diverse features of microbes include morphology, ecological niche, nutrient sources and physical survival capabilities 3. microbes outside the lab typically live in temperate, nutrient - poor conditions and are embedded in microbial communities.
prokaryotic cell envelope cytoplasmic cell membrane, outer membrane, cell wall, s-layer, mycomembrane
cell envelope essential functions permeability barrier, protein anchor, energy conservation
protein anchor site of protein that participate in transport, bioenergetics, and chemotaxis
energy conservation site of generation and dissipation of proton motive force
cell membrane of bacteria phospholipid bilayer. hydrophilic glycerophosphate head. hydrophobic tail of two fatty acid chains. linked by ester bonds
archaeal cell membrane ether linkages between head and tails. isoprenoids instead of fatty acids. can be monolayer. stable than bacterical membranes
cell walls protects from membrane - destabilising chemicals. resists osmotic pressure, created by the very high concen. of salts and small molecules in the cytoplasm.
bacterial cell walls made up of peptidoglycan. peptide chains and glycan chains
peptidoglycan cell walls repeating glycan units of N-acetylmuramic acid and N-acetylglucosamine acid, cross linked peptides. creates strong, flexible and porous structure encasing the cell.
how do peptide components vary between bacteria? cross-linked with each other, directly or via a bridge. includes on-standard amino acids, D isomers, diaminopimelic acid and others
gram positive cell walls single membrane. thick peptidoglycan cell wall (thick layer). cell exterior also contains teichoic acids which promotes surface attachment and host interaction.
gram negative cell walls thin peptidoglycan layer. outer membrane. braun lipoprotein tethers outermembrane to peptidoglycan. periplasm = compartment between inner and outer membranes.
what is in the outer membrane of gram negative cell walls? inner layer of phospholipids. outer layer with high amounts of lipopolysaccharides. impermeable to proteins and large molecules. porins allow diffusion of small molecules, large molecules require dedicated transport systems.
lipopolysacchride lipid A component is toxic to many animals. important disease (AKA endotoxin). O-specific polysaccharide is highly variable. helps create permeability barrier to bile salts, antibiotics, etc. helps protect from the immune system.
what is periplasm? separates compartment of gram negative cells, about 15nm wide. synthesis of cell wall components. degradation of large polymers. OM prevents useful extracellular enzymes from diffusing away.
distinguishing G+ and G- G+ cells = purple because thick peptidoglycan cell walls retain crystal violet - iodine complex. G- cells = do not retain crystal violet = pink
exceptions to staining mycobacteria is G+ - highly resistant waxy mycolipid outer layer makes staining variable. mycoplasma is G+ - lacks a cell wall, but has membrane sterols provide extra rigidity.
archaeal cell walls polysaccharides similar to peptidoglycan. s-layers.
s-layers permeability barrier. cell-shape/structure. immune interaction/evasion. weaker than peptidoglycan. always outermost layer
drugging cell envelope lysozyme. penicilins. cephalosporins. lipopeptides.
lysozyme degrades peptidoglycan
penicilins prevents peptidoglycan synthesis
cephalosporins prevents peptidoglycan synthesis
lipopeptides disrupt membranes
WEEK 2, PART 1 - SUMMARY 1. G+ bacteria have a single membrane and a thick peptidoglycan layer. 2. G- bacteria have a cytoplasmic membrane. thin peptidoglycan layer, and an outer membrane. 3. most bacteria have surface polysaccharides, which provides extra function/protection
WEEK 2, PART 1 - SUMMARY 2 4. archaea usually have a proteinaceous s-layer cell wall, which, together with the most stable archaeal membrane, provides sufficient strength.
cell surface structures capsules/slime layers. flagella and archaella. pili
sugary armour: prokaryotic capsules polysaccharide layer surrounding cell: called a capsule if tightly packed and attached. or called slime layer if looser.
do capsules change? changes in response to environmental cues
capsule properties capsule masks the cell surface. capsule is hydrophilic and retain water. capsule slows diffusion near the cell surface. capsule is sometimes sticky. capsule does not provide structure to the cell.
capsule masks the cell surface function immune evasion
capsule is hydrophilic and retains water function desiccation resistance
capsule slows diffusion near the cell surface function nutrient aquisition
capsule is sometimes sticky surface attachment, biofilm formation
bacterial flagellum powered by proton motive force.
parts of flagellum long (5-10um) hollow filament made of flagellin proteins, new ones add to the tip. hook connects the filament to the basal body. basal body complex (approx 15 proteins) anchor structures across all layers of the cell wall/membranes --> proton motive force
archaellum propel cells through liquid.
parts of archaellum filament narrower and not hollow. no hook/basal body: anchored by a complex of just a few proteins in the cytoplasmic membrane. not proton motive force: ATP provides energy for rotation
pili structure thin (2-10nm) filamentous protein structures that extend from the cell. bacteria and archaea
pili functions attachment. motility. genetic exchange (conjugation, transformation)
genetic exchange - conjugation genetic transfer between donor and recipient cells
genetic exchange - transformation uptake of DNA directly from the environment.
surface structures as antigens surface exposed parts of bacteria can be recognised by the immune system, and by bacteriophages
surface features are the target of serotyping, which classifies bacteria based on reaction with antibodies against known types. vaccines. monoclonal antibody drugs.
WEEK 2, PART 2 - SUMMARY 1. capsule is protective, highly variable polysaccharide coat produced by many bacteria and some archaea. 2. flagellum = proton powered rotary motor in bacteria 3. archaeallum =ATP powered rotary motor in archaea, evolved from pili
WEEK 2, PART 2 - SUMMARY 2 4. both bacteria and archaea prod diverse pili: attachment, twitching, motility*, conjugation* and transformation. *= only known in bacteria
nucleoid bacteria and archaea do not have a membrane-bound nucleus. DNA is still very tightly organised and packed. genome and packing proteins = nucleoid
how big are prokaryotic genomes? archaea= 0.5-6 MB bacteria = 0.5-15 MB
DNA packaging in bacteria DNA is supercoiled. organised in a 'bottlebrush' structure. long, supercoiled loops tethered by specific proteins. specific nucleid associated proteins (NAPs) bind to the chromosome. both structural and regulatory roles. small and positively charged.
DNA packaging in bacteria types DNA bending, stiffening, bunching, bridging, wrapping
prokaryotic cytoplasm site of translation and metabolic reactions. extremely crowded. cytoskeletons. inclusions
inclusions storage compartments. metabolic compartments. gas vesicles. endospores.
storage compartments phosphate, carbon, sulfur, and other minerals stored in cytoplasmic granules. membrane enclosed.
gas vesicles dormant, highly resistant cells. low H2O content, multiple protective protein and membrane layer. tolerate extreme heat, drying radiation and chemical exposure
importance of endospores allows bacteria to colonise new distant environments, even if the conditions in between would kill the vegetative cell (e.g. strict anaerobes in the gut). contribute to food spoilage. contribute to spread of some pathogens.
eukaryotic micoorganisms protists, fungi
one of the largest eukaryotic microbe Paramecium sp.
protists that produce cell walls of cilica diatom frustules
fungi, long multicellular filaments, have spores - get released into the air Penicilum sp.
common features of eukaryotic cells structurally complex and larger - compared to bacteria/archaea. cell membrane. lack cell wall in animal kingdom. cell wall vary in protists,
endomembrane system nucleus, nucleolus, ER, golgi apparatus, lysosomes
cell envelope and cytoskeleton plasma membrane, lack. have a chemically distinct cell wall, Cytoskeleton
chemically distinct cell wall examples photosynthetic algae have cellulose, pectin and silica. fungi has chitin and glucan.
cytoskeleton composition interconnected filaments. microfilaments (actin), microtubules, intermediated filaments and motor proteins
mitochondria mitosomes. double memb.
mitosomes from mitochondria. found in some protists. no mtDNA, ETC and OP. Fe and S cluster assembly
hydrogenosomes some anaerobic protists. double memb. no cristae. lack DNA. ATP through fermentation. CO2, H2 and acetate = products
cilia short, membrane bound cylinders. axoneme. basal body
protists taxonomic classification is always changing. unicellular. found in moist environments. some recycle nitrogen, phosphorus, decaying organic matter.
heterotrophic protists saprophytic nutrition. holozoic nutrition.
saprophytic nutrition nutrients obtained from dead organic matter through enzymatic degradation. osmotrophy - absorb soluble products
holozoic nutrition solid nutrients acquired by phagocytosis
phototrophic protists strict aerobes, use of photosystem I and II for oxygenic photosynthesis
mixotrophic protists both
protozoan morphology plasma membrane. pellicle (support). cytoplasm. cilia/flagella/pseudopodia. free living/parasitic.
parasitic protists most free living. causes diseases. e.g. malaria
survival of protists encystment, excystment
encystment protist simplify in structure, become dormant (cyst) with a cell wall and low metabolic activity.
what does cell wall of a protists cyst do? protects against environmental changes. can assist in nuclear reorganisation/reproduction. serve as a means of host to host transfer for parasitic species.
excystment return to favourable conditions may stimulate a cyst form to its original state. parasitic protists - may occur following ingestion of a cyst by a new host organism
protist reproduction asexual: binary fission sexual: syngamy process - gamete fusion
archaeplastida taxonomic group. red algae (rhodophytes). green algae (chlorophytes and charophytes).
taxonomy of protists archaeplastida. amoebozoa. opisthokonta. rhizaria. Chromalveolata. excavata
mycology branch of microbiology studies fungi
fungi yeast and mold
mycoses disease by fungal infection
good fungi budding yeast: baker's and brewer's yeast. bioethanol production agriculture. antibiotics. decomposition
bad fungi potent allergens. foul smelling. poisonous/toxins. hallucinogens/deathly. food spoilage
molds multicellular. hyphae - grow from tips. mycelium. asexual spore = conidia.
fruiting bodies tight mesh of hyphae. prod spores cast through gills into environment. mushrooms eg of fruiting bodies
types of conidia arthrospores, conidiospores, sporangiospores, chlamydiospores, bastospores
conidia asexual spores
sexual reprod of fungi - fusion homothalic, heterothalic.
homothalic formed same mycelium
heterothalic diff mycelium
sexual spores of fungi ascospores, basidiospores, zygospores
yeasts single- celled. fission yeast, budding yeasts. facultative anaerobes.
facultative anaerobes oxygen available = aerobic resp. oxygen not available = fermentation
fungi taxonomy chytridiomycetes, glomeromycetes. zygomycetes. ascomycetes/sac fungi. mushrooms and other basidiomycetes.
do viruses have DNA some do, they can be double stranded, single stranded, gapped, linear and circular
do viruses have RNA many viruses do not have RNA that are double stranded and single stranded. can be non segmented/segmented
baltimore classification virus types 1. dsDNA 2. ssDNA 3. dsRNA 4. positive sense RNA 5. negative sense RNA 6. retroviruses 7. gapped dsDNA
what is a virion infectious particles, to replicate they must enter the cell
5 common stages of the viral life cycle 1. attachment 2. penetration and uncoating 3. synthesis 4. assembly 5. release
stage 1 of viral life cycle 1. attachment - recognise and attach to specific target cell/tissue
stage 2 of viral life cycle 2. penetration and uncoating - enter the cell and uncoat capsid/release the genome payload: access to cellular components
stage 3 of viral life cycle 3. synthesis - gene expression/replication, genome directs synthesis of virion components (protein and nucleic acid)
stage 4 of viral life cycle 4. assembly of virion, largely self-assembly of structural subunits (genome and protein) and packaging of nulceic acid
stage 5 of viral life cycle 5. release of virions (budding, lysis)
attachment in detail receptors are bound by viral surface proteins - naked (part of capsid/shell), envelope (glycoprotein in membrane)
penetration and uncoating in detail 3 methods: - injection of nuclei acid. - fusion of the viral envelope with host membrane (enveloped viruses) - endocytosis in vesicle; endosome aids in viral uncoating
how do bacterial viruses penetrate generally direct injection into cell via ejection from the capsid -- penetration of the cell wall and ejection of DNA into cytoplasm
how do animal viruses penetrate fusion of the virus at the plasma membrane, endocytosis (followed by fusion if enveloped virus or pore formation/ysis for naked virus)
eneveloped viruses fusion fusion of viral envelope with the plasma mebrane
enveloped virus endocytosis endocytosis is followed by fusion of viral envelope with endosome membrane and delivery of content to the cytoplasm
naked virus endocytosis - cannot fuse, so endocytosis followed by release from endosome into the cytoplasm - formation of pores or disruption of endosome
synthesis in detail transcription (nucleic acid genome to mRNA), replication (genome to genome)
lytic infection productive infection ( can cause cell lysis)
latent/lysogenic long term infection in which the viral genome is maintained with limited expression of viral genes and without loss of host cell viability
lytic cycle lytic and temperate phage - phage injects DNA, repliates, lyses the host cell, releases progeny phage
lysogenic cycle temperate phage only - phage injects its DNA, DNA integrates into the host cell chromosome. page DNA (prophage) is then replicated with the host chromosome. genotoxic stress or other stimuli - reactivates, re-enters lytic/reproductive
nutritional requirement for microorganism proteins, lipids, carbohydrates, nucleic acid.
carbon acquisition - Macromolecules are formed from the condensation of organic carbon monomers. - Autotrophs (primary producers) fix carbon dioxide into organic carbon (enzymes like rubisco) -Heterotrophs (consumers) recycle organic carbon released by other organisms
Nitrogen acquisition 80% of the atmosphere is nitrogen. Triple bonds Diazotrophic bacteria fix atmospheric N2 into aqueous ammonium. Other microbes acquite nitrogen from other sources (e.g. ammonium, nitrate, dead biomass)
Other nutrients Microbe also have a range of stratergies to get other important building elements including: phosphorus (nucleic acids, phospholipids) Sulfur (amino acids, vitamins) Metal (Fe, Mg, Na, K, Ca, Mn, Cu, Zn, Ni)
ATP Adenosine triphosphate - ATP serves as the main store of chemical energy in bacteria, archaea, and microbial eukaryotes. Its phosphodiester bond releases a large amount of free energy when hydrolyzed.
HYDROLYSIS Chemical reaction in which a water molecule is used to break down a larger molecule into smaller molecules. Hydrolysis in cells: Proteins → amino acids Nucleic acids → nucleotides Carbohydrates → monosaccharides
process of hydrolysis Water molecules are split into hydrogen ions (H+) and hydroxide ions (OH-) They react with other molecules to form ne compounds
anabolism Cells use energy released by ATP hydrolysis to synthesise macromolecules. ATP also used for other work, e.g. motility and active transport
Catabolism Cells use energy from the environment to make ATP. Two main energy sources: light (photosynthesis) and chemicals (chemosynthesis)
microbes make ATP via chemiosmosis ATP synthase produces most of the ATP in most microorganisms. Primary pumps generate this proton gradient. They use energy derived from sunlight (photosynthesis) or organic/inorganic chemical (chemosynthesis) to pump protons to the periplasm
what is chemiosmosis A biological process that occurs in cells – energy is generated by the movement of ions across a membrane. Involves the coupling of electron transport and ATP synthesis through the generation of a proton gradient.
rhodopsins example of a proton pump -- photosynthetic and chemosynthetic microorganism use numerous strategies to generate proton gradients.
organic electron donors (organotrophy) carbohydrates, lipids, proteins, lignin, methane, hydrocarbon, xenobiotics
inorganic electron donors (lithotrophy) hydrogen gas, carbon monoxide, formate, ammonia, nitrite, sulfide, iron
classification 1 - energy source Phototroph = sunlight Chemotroph = chemicals
Classification 2 = ELECTRON DONOR Lithotroph = inorganic compounds Organotroph = organic compounds
Classification 3 = CARBON SOURCE Autotroph = carbon dioxide Heterotroph = organic carbon
Obligate aerobes For example many heterotrophic and iron oxidsing bacteria, require oxygen to grow. They use aerobic respiration to grow Thrive in environments such as soil, freshwater, and marine waters.
Obligate anaerobes For example sulfate-reducing bacteria, methane-producing archaea, and green sulfur bacteria, grow only in the absence of oxygen. anaerobic respiration and/or fermentation to grow. Thrive in environments such as gastrointestinal tracts.
Facultative anaerobes Including E. coli and many pathogens Flexible organisms that grow by aerobic and anaerobic respiration
Fermentation – results in incomplete organic carbon oxidation Many organotrophs conserve energy through fermentation This results in incomplete organic carbon oxidation Endproducts are excreted e.g. ethanol (Saccharonyces), lactate, and mix acids
How do fermenters make ATP? – substrate- level phosphorylation. Through the glycolytic pathay In this process, enzymes directly transfer phosphoryl groups from an activated substrate to ADP
fermentation process yields much less ATP than respiration: glucose --> 2 pyruvate --> either lactate fermentation or ethanol fermentation
two key proteins that control E.coli division An actin like protein promotes cell elongation. A tubulin like protein promotes fission
actin like protein Mreb, a protein homologous to eukaryotic actin, forms a simple cytoskeleton around E. coli cells. This maintains their size and shape. This protein promotes cell wall synthesis and chromosome separation during growth
tubulin like protein FtsZ, a protein homologous to eukaryotic tubulin, polymerises into a ring around the centre of the cell following elongation. The constriction of this ring through depolymerisation triggers partitioning into two daughter cells (cytokinesis)
four major phases of microbial growth lag phase, exponential phase, stationary phase, death phase
lag phase Cell prepare for growth (e.g. enzyme synthesis). No duplication occurs despite high nutrient support
Exponential phase Cells grew rapidly by binary fission and consume available nutrients. Most cells are living.
stationary phase Cells number peak as nutrients become scarce. Number of live cell equal of number of dead cells.
Death phase Cell numbers declining and more dead cells than live. Nutrient exhausted, acids and waste increase.
Calculation of general time Measure the time taken for the population to double during exponential phase
extremophiles mesophiles, psychrophiles, thermophiles, xerophiles, halophiles, acidophiles, neutrophiles, alkaliphiles
mesophiles moderate temps
psychrophiles very cold temps Protein and membrane content = more fluid DNA content = more AT bases - two H bonds Chaperone = cryoprotectant solutes to reduce ice formation
thermophiles very high temps Protein and membrane content = more rigid DNA content = more GC bases - three H bones Heat-shock proteins to reduce denaturation
xerophiles low water
halophiles high salt
acidophile low pH, 5.5
neutrophile neutral pH
alkaliphile high pH, 8.5 - 11
GOAL 2 ZERO HUNGER Microbes as crop growth boosters - Plants such as soybeans gain nitrogen from Nitrogen-fixing microbes associated with their roots, which convert N2 gas into useable NH3
GOAL 2 ZERO HUNGER p2 Microbes as food spoilage agents Fresh food supports the growth of various microbes eg. Pectobacterium bacteria damage potato crops, sometimes causing big losses
GOAL 2 how can microbiology help? boost nitrogen fixation to improve crop yields prevent microbial disease of crops Producing nutrient-dense foods by microbial fermentation rumen microbiome to increase production of food molecules for the animal while reducing methane production
goal 3 good health and wellbeing
goal 3 how microbiology can help? Monitoring existing and new infectious disease threats Preserving our antibiotics and discovering new ones Understanding how the microbiome affects health, and designing interventions Developing microbial therapeutics such as phage and probiotics
goal 14 life below water
goal 14 how can microbiology help efficiency of microbial bioremediation in the ocean Understanding the thresholds for eutrophication, in order to prevent it from happening Research aimed at maintaining essential microbial nutrient cycles in the oceans
Created by: redshre
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