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University of Waterloo
BIOL 240
Josh Neufeld

BIOL 140 Complete NotesModule 1 IntroductionLecture 1 MaterialWhy Study MicrobiologyFirstly what is microbiologyHow old is this fieldAnd what did this study give rise tooIt is the science of microorganisms organisms that are very small and unicellularoIt is only a century old before then microscopes werent powerful enoughoMicrobiology has given rise to molecular biology and biotechnologyWhat phylogenic domains include organisms which are considered to be microbesoProkaryotic domains archaea and bacteriaoEukaryotic domains algae fungi and protozoaWhat are fundamental processes which microbes like all other organisms participate in Expound on each as necessaryoMetabolism take up nutrients make energy use energy etcoReproduction make new cells binary fission is a biggie in this fieldoDifferentiation creating a new cell structure UNidentical from the old one ie spore productionoCommunication sending chemicals back and forth to act as signalsoMovement think about flagella etcoEvolution this is what phylogenetic trees are all aboutExplain how microorganisms set the stage for life on earth as we know it todayoThey were the first life on earth because they were able to tolerate a wider variety of environmental conditions than we canIn particular bluegreen algae called cyanobacteria came first because they didnt need oxygen and could extract energy from the sunNote that even cyanobacteria had to come from some universal ancestor that eventually gave rise to all organisms phylogenetic trees show us that everything is related on at least SOME leveloEventually their cellular processes ie the production of oxygen created a biosphere where we could surviveoWhen this happened multicellular organisms evolved from microorganismsTalk about microorganisms now and in the futureoMore than 50 of the biomass on earth is microorganisms ie if you take all the carbon and weigh itoMicroorganisms will be on earth forever because they are so diverse and easily adaptable that they can handle any change in living conditionsName and comment on 5 major areas of applied microbiologyoAgriculture there are many microbiological processes which are essential in agricultureFor example bacteria accumulate in the root nodules of alfalfa plants and fix nitrogen which means they turn nitrogen into ammonia which is needed by the plant to growThis saves the farmers from having to use fertilizer which is damaging to the environmentoEnergyenvironment microbiological processes can be used to make fuels ie cornethanol to clean up pollutant spills by consuming the undesirable substance and so onoDisease lots of diseases especially infectious ones have a microbiological basis and so understanding and research of microbiology in this respect can help us cure the diseasesoFood microbiology helps us to understand why we have to preserve foods etcoBiotechnology this is a HUGE area where we use microbes to do technological things for us such as gene therapy the creation of insulin by giving the gene to bacteria etc1 Lecture 2 MaterialThe Historical Roots of MicrobiologyWhat did Pasteurs famous experiment proveoRather it DISproved the theory of spontaneous generation the idea that when for example food was left out in the open the bacteria which grew came from nowhere ie they formed spontaneouslyoThus what he actually did was PROVE that we need a preexisting organism in order to form a new oneHow did he achieve thisoHe achieved this by using a special flask called a Pasteur flask where the neck was curved such that air from the outside could not get into the broth which was kept in the bowl of the flaskoHe then sterilized the broth by heating it heat kills almost all bacteria and then just let it sit thereoIt was demonstrated that nothing grew in the brothWhyBecause nothing from the air could get to itoThen when he tilted the flask so that air could get to the brothand when he did so tons of stuff grewWhat were Kochs postulatesoYou should know this from HLTH 341Why did he develop them and what did they help him to concludeoHe developed them when he was working on Anthrax and trying to determine whether a certain bacterium called Bacillus anthracis caused anthraxoHe eventually concluded that it DIDoIn general the idea here is that specific organisms cause specific diseasesTalk very briefly about characteristics which prokaryotes and eukaryotes share and things they do NOT shareoThey are both surrounded by a cell membrane which separates the outside of the cell from the cytoplasmoEukaryotic cells differ from prokaryotic cells in that they contain membraneenclosed structures organelles within them prokaryotes have nothing inside them which is membraneenclosedThese include mitochondria chloroplasts and the nucleusoIt is also notable that eukaryotic cells are on average much bigger than prokaryotic cells which in turn are much bigger than virusesQuickly characterize viruses and explain how they are different from cellsoThey are not cells They dont have open systems for taking in nutrients and expelling wasteThey cant reproduce on their ownThey dont moveoBasically they are particles of genetic material which are only of any consequence when they enter a cell in which case they can use the cells biosynthetic machinery to do stuff most notably to replicateoThey have been known however to infect ALL types of cellsQuickly comment on ribosomal RNA gene sequencingWhat is the name for this practiceoOK so the idea is that looking at ribosomal RNA part of ribosomes is very useful for determining evolutionary relationships between organismsOne reason why rRNA is good is because all organisms have it because all organisms have ribosomesoSo PHYLOGENY is the practice of isolating rRNA from different organisms looking at their sequence then making conclusions about how close the organisms are related based on how similar their rRNA sequences areWhat are the 3 domains of lifeWhich families belong in eachComment on some general relational trends2oSee Figure 27 pg 27oThere are two distinct lineages of prokaryotes the Bacteria and the ArchaeaThe Archaea are actually more closely related to the Eukarya than they are to the BacteriaoAnywhere on a phylogenetic tree a clade is a group of organisms with a common ancestor Module 2 The Diversity of MicroorganismsLecture 3 MaterialThe Physiological Diversity of MicroorganismsOK what are the two things that microorganisms need to get in order to surviveoEnergy for cellular processes and carbon for building stuffTalk about the different names for organisms based on how they get these thingsoChemotroph vs phototroph chemotrophs get energy from chemicals while phototrophs get energy from lightoChemoorganotrophs vs chemolithotroph chemoorganotrophs get their energy from organic substances while chemolithotrophs get their energy from inorganic substancesoHeterotrophs vs autotrophs heterotrophs get their carbon from preexisting organic compounds while autotrophs get their carbon by fixing CO2Notably most phototrophs are autotrophs makes sense that they dont need actual substances for either carbon or energy rightAlso note that photoautotrophs are primary producers because they produce new organic matter from just carbon dioxide and thus other organisms can feed off thisDescribe how organisms can also be classified based on the environments which they thrive inoThis is particularly relevant for extremophiles which are microorganisms which thrive in extreme conditions such asHigh temperature hyperthermophileMedium high temperature thermophileLow pH acidophileHigh pH alkaliphileHigh pressure barophileHigh salt environment halophileWhich phyla are present in the domain BacteriaComment where appropriate on eachoProteobacteria a lot of chemotrophs here both organo and lithooGrampositive bacteria test positive for the Gramstainit means they have a similar cell wall structureoCyanobacteria they do photosynthesis thus producing oxygen for us and they are very visual we can see them easilyoPlanctomyces they have a characteristic stalk shapeoSpirochetes they are in a spiral shapeoGreen sulfur and nonsulfur they are photosyntheticoAquifex thermotoga they are found in high temperature environmentsoEnvOP2 we cant culture these we only know they exist because we have sequenced their rRNAthe same applies to SAR11 which we saw in a videoNow for the domain archaeaGive a general overview of phylogenetic structures we see hereoFirstly the domain can be split into 2 subdomains euryarchaeota and crenarchaeotaoThe euryarchaeota subdomain has 3 groupsMethanogens strict anaerobes who produce methaneHalophiles strict aerobes who like very salty environmentsAcidophiles grow best at low pH3
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