Environmental microbi BIOSCI204 FINAL EXAM PREPARATION. Microbiology in nutrition, growth and metabolism

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1 BIOSCI204 FINAL EXAM PREPARATION Microbiology in nutrition, growth and metabolism Microbial nutrition Microbial growth Control of microorganism in the environment Microbial metabolism: Energy, enzymes and regulation Microbial metabolism: Energy release and conservation Microbial metabolism: The use of energy in biosynthesis Evolution and genetics The origins and evolution of microbial life Genome replication and gene structure Gene expression Gene regulation in prokaryotes Gene regulation in eukaryotes Environmental microbi Macro meets micro: eco microbes Genes to genomes: mic genomics and its applic Microbial symbioses Microbe in extreme environments Biogeochemical cycling Microbial impresario Microbial biotechnology Energy and waste Microbial production of additives Microbial foods Microbial role in agricul Microbes and water sup water restoration EXAM: Two essay questions from each

2 Microbiology in nutrition, growth and metabolism! Microbial nutrition 1 What basis nutrients are divided into macroelements and trace/microelements. Marcoelements: proteins, lipids, carbohydrates, nucleic acids, cations in water. Microelements : Mn, Zn, Co, Mb, Ni, Cu and growth factors (vitamins, amino acids and silicon) 2 The ways in which microorganisms are classified based on their requirements for energy, carbon and electrons. Carbon sources Autotrophs : Use sole!!! or biosynthetic carbon source to produce organic complex. Heterotrophs: Cannot fix carbon, use organic carbon to grow. Energy sources Phototrophs : Light Chemotrophs: Oxidation of inorganic or organic compounds Electron sources conservation (e.g. ATP production) Organotrophs: Obtain hydrogen or ele from organic compounds 3 How microorganisms obtain carbon, nit phosphorous and sulphur to grow. ABC (ATP-Binding-Cassette) transporte Substances bind on solute-binding protei protein binds to transporter, it allows sub across to the cytoplasmic membrane. Als nucleotide-binding domain, ATP is hydrol ADP+ P. 4 Distinctive characteristics and mechani active transport and group translocation Active transport using proton and sod ingredients (secondary transport): Protons are pumped outside of the plasm membrane during electron transport. The of protons drive the expulsion of sodium port mechanism. Sodium binds to carrier complex resulting to conformational chan solute binding site. So that the sugar or is able to bind. Then solute is transported of plasma membrane by symport mecha Phosphoenolpyruvate: sugar Phosphotransferase system (PTS)

3 phosphorous to G6P and M1P. Transport of carbohydrate in Fungi: free diffusion, facilitated diffusion and active diffusion. Transport of carbohydrate in Bacteria: Permease system, PEP-PTS system. Iron uptake: Sideronphores 5 The characteristics and use of different types of media Minimal media: grow wild type Defined media: all chemicals are known Complex media: undefined, carbon source, salts, amino acids and nitrogen source Supportive media: liquid, defined and general purpose Enriched media: nutrients contained to grow a wild variety Selective medial: only grow selective microorganism Differential media: distinguish one microorganism type from another growing in the same media 6 The definition and significance of pure cultures Pure culture: only one species. Developing pure culture is crucial to the observation of the specimen in research! Microbial growth 1 The differences and similarities betwee prokaryotic and eukaryotic cell cycles 1. Average euk has 25 times more D pro 2. Pro has one point of origin, replic occurs in opposing direction and occurs in cytoplasm. Whereas pro multiple points of origin, replicati undergo undirectionally and take within nucleus. 3. Pro possess one or two type of p whereas euk has four or more ty 4. Replication rate of pro is much fa euk. 5. Euk has distinct process for replic telomeres at the end of their chro pro has no ends to synthesise. 6. Short replication of pro occurs alm simultaneously but euk only goes phase of cell cycle. 2 The cause of four phases of the growth close system

4 other molecules occurs. Exponential (log) phase: A period characterised by cell doubling. Stationary phase: Due to growth-limiting factor such as the depletion of an essential nutrient and/or the formation of an inhibitory product such as organic acid. Death phase: Bacteria die due to lack of nutrients. A temperature which is too high or too low or wrong living conditions. 3 Each technique by which microbial population numbers may be determined and give its advantages and disadvantages. Petroff-Hausser counting chamber:!!"##$/!!! = (!"##$/!"#$%&) (25!"#$%&!) 50 10! Colony forming units (CFU): Full=TNTC, 30~300, <30 TFTC CFU=!"#$%&!!"!!"#"$%&'!"#$%"&'!!"#$%&!!"#$%&!!"##!!"!!"#$%& Spectrophotometer: Dry weight g/l or mg/ml 4 How open system differ from a closed culture or batch culture Chemostat: continuous culture unit: - growth controlled by dilution rates - slow flow rates slow growth rates - fast flow rates fast growth rates microorganisms Obligate aerobe: completely depen atmospheric oxygen for growth Facultative anaerobe: not require o better growth with oxygen Aerotolerant anaerobe: grows equa with or without oxygen Obligate anaerobe: does not tolera presence of oxygen Microaerophilic: require oxygen lev 2~10% for growth, damaged by atmosph of oxygen(20%)! Control of microorganism environment Sterilization: Totally free of viable microorganisms, spores and other infect Disinfection: Killing, inhibition or rem microorganisms that may cause disease (Disinfectants). Sanitization: Reduction of microbial safe level (Sanitizers, Pasteurization). Biocides: A chemical or physical age broad spectrum) that inactivates microor Antiseptics: Agents that prevent infe sepsis. Suffixes: cide: kill static: stop Physical control: heat -Moist heat: Pasteurization, Boiling,

5 Physical methods: Radiation; Ionizing: X-ray, Gamma radiation, Cathode; Non-ionizing: Ultraviolet (260nm, cuse T-T dimerization, does not penetrate solids or liquids): Disinfection. Mechanical removal: filtration -Membrane filter -Depth filter -HEPA filter Chemical methods: Gases (Sterilization, Disinfection); Liquids (Animate: Chemotherapy, Antiseptics; Inanimate: Disinfection, Sterilization) Phenolics (Phenol, Orthocresol, Triclosan, and Hexachlorophene): Denature protein, dissolve membrane lipids. Alcohols(Ethanol, Isopropanol): Denature protein, dissolve membrane lipids. Halogenated compound (Halazone): Oxidation of cellular material. Aldehydes (Formaldehyde, Glutaraldehyde): Inactivates nucleic acids and protein. Quaternary ammonium compounds :( Cetylpyridinium, Benzalkonium): Disrupt microbial membranes and proteins. Gases (Ethylene oxide, Betapropiolactone, Hydrogen feroxide): e.g. EtO blocks functional groups of DNA and proteins. The decimal reduction time (D): The time required to kill 90% of the microorganisms or spores in a sample under specified conditions. value required to reduce the microorgani population by 90 %(one log unit) Triclosan: Used since 1968, mostly ( personal care products, a ubiquitous poll waterways. Monde of action: Binds and inhibits E enzyme used in fatty acid synthesis; Enc Fabl gene (not found in humans). Resistance mechanism: Fabl mutatio alternative Fabl genes (Fabk) reduce tric effect, some bacteria over express Fabl, efflux pumps remove triclosans from cell Bacteriophage is a virus that can inf Phage therapy developed and still been u -Advantages: Alternative to antibioti very strain specific -Disadvantages: Poorly studied and able to develop resistance/immunity! Microbial metabolism: Ene enzymes and regulation 1 Metabolism, energy, energy-conserving catabolism, anabolism and reducing pow Metabolism: building up and breaki Catabolism: breaking down Anabolism: building up

6 phosphorylation) or endogenous reaction electrons). Pyruvate is used as electron a and the final products are ethanol, hydro lactic acids. 2 The benefits for a microbial with the Em Meyerhof pathway and tricarboxylic acid pentose phosphate pathway. 6 Three ways metabolic pathways may be regulated Control of enzyme activity Metabolic channelling Inhibition controlling! Microbial metabolism: Energy release and conservation 1 Compare and contrast respiration and fermentation, giving example of the types of electron acceptors used by each process For respiration process, the source of the process undergoes electron transport chain, the PMF (proton motive force) drives oxidative phosphorylation to yield ATP. Also, products are made. To be specific, oxygen are electron acceptor for aerobic respiration and!!!!!,!!!!,!!!,!"#$%$&' etc. for anaerobic respiration. Glycolysis is amphibolic and found major groups of microorganisms occurrin cytoplasma, which active in the presence absence of oxygen. It is used mainly by soil microbes, and very few Gram +ve ha pathway. Glucose + 2 ADP + 2 Pi + 2 NAD+ 2 pyruvate NADH + 2 H+ Pentose phosphate pathway (PPP in cytoplasma can be active simultaneou glycolysis or Entner-Doudoroff pathways in the presence and absence of oxygen. important in biosynthesis. Glucose 6-P + 12 NADP+ + 7 H2O 6 CO2 NADPH + 12H+ + Pi Tricarboxylic acid cycle (TCA) is providing the source of energy and carbo for biosynthesis. It occurs in cytoplasm in prokaryotes and mitochondrial matrix in For each acetyl CoA oxidised the cycle generates!2!! 2, 3!"#$, 1!"#! 2!!"#!1!"# is not present in strict anaerobic and