Microbial Evolution

Henry Lynch
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MICR222 Flashcards on Microbial Evolution, created by Henry Lynch on 07/16/2018.

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Henry Lynch
Created by Henry Lynch over 1 year ago
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Question Answer
What are three key events in the Earth's evolution related to microbial evolution? - Origin of photosynthetic bacteria - Development of aerobic respiration and oxygen rich atmosphere (extinction of some anaerobes) - Origin of eukaryotes
What was the conclusion of the Miller-Urey experiment (1950s)? The organic building blocks of life are generated in the probable atmosphere of early earth
Describe the characteristics that were thought to have made up the atmosphere of early earth Anoxic High temp High UV Alternative energy forms (geothermal, radiant etc.)
Molecules that made up the early Earth's atmosphere most likely had what tendencies? They were aggregates and/or membrane-like interfaces
Give a bief description of a Coacervate? Liposome vesicle structures that are an early example of a cell wall These grow by the aggregation of polymers forming a semipermeable membrane allowing division upon size The semipermeable membrane allows for the formation of a pmf leading to the creation of energy for life
Describe the 'central dogma' of biology Explains flow of genetic info from DNA to RNA to Protein (product) https://www.yourgenome.org/facts/what-is-the-central-dogma
The first organism must have had what two characteristics? Anaerobic Chemolithotrophic (FeS and H2S)
How is diversity measured in microbial communities? Through: - Taxonomy - Function - Metabolism
What three methods do we use to classify microbial diversity? and describe each Biological - group based on ability to breed Phenetic - based on similatirities with no account of evolutional history (liable to errors due to convergent evolution) Cladistic (phylogenetic) - based on evolution from shared ancestors (liable to ignore descriptive trait)
What sequence is most commonly used as a measure of evolutionary divergence? 16S rRNA sequence
Describe the role of decomposers (fungi) Convert dead organic material into fungal biomass, CO2, and small molecules such as organic acids. Use complex substrates (cellulose and lignin in wood) and are essential in decomposing the carbon ring structures in some pollutants.
Define 'absorptive nutrition' in fungi Describes a way of obtaining energy and nutrients in which digestive enzymes are secreted into a substrate, then smaller, easily assimilated molecules are absorbed through the cell membrane.
Describe the role of mutualists (fungi) Colonise plant roots to help solubilise phosphorus and bring soil nutrients to the plant in exchange for carbon from the plant.
Describe the role of pathogens (fungi) Cause reduced production or death when they colonise roots or other organisms
What are some characteristics of heterotrophs as decomposers? Break down carbon substrates Most common group Convert energy in soil matter into forms useful to the rest of the organisms in the soil food web Break down pesticides and polutants Immobilise nutrients in their cells preventing loss E.g. - Proteobacteria, Acidobacteria
What is the electron source and carbon source of an autotroph? Hydrogen sulfide as the electron source Carbon dioxide as carbon source
What is the most well known form of Mutualist? Nitrogen fixing bacteria
Define 'Species' A group of organisms capable of interbreeding and producing fertile offspring of both genders
Describe what DNA-DNA hybridization (DDH) measures Measures the degree of genetic similarity between complete genomes by measuring the amount of heat required to melt the hydrogen bonds b/w base pairs of the double helix DNA
Besides measurement, what does DDH provide? Provides a standardised means for classifying prokaryotes that lack well defines morphological or phenotypic characteristics
What are the limitations of DDH? Time consuming Only carried out by a few labs Ill-suited for rapid identification Only suited for pair-wise classification Unavailable for non-culturable organisms
What output values from DDH are considered a species match? >70% binding value and >97% 16S rRNA gene sequence similarity
What output values from DDH infer different species? <50% binding value
What are some caveats of 16S rRNA gene comparison? Lacks resolution compared to DDH Cannot discriminate between highly related species Does not relate to metabolic capabilities Relies on single gene 16S rRNA can be too conserved (slow evo.)
What is the purpose of Multilocus Sequence Typing (MLST)? A method for the GENOTYPIC characterisation of prokaryotes at the infraspecific level, using the allelic mismatches of a small number of housekeeping genes. Used for recognition of distinct strains within named species.
MLST is the precursor to what? Multilocus sequence analysis (MLSA) - a method for the GENOTYPIC characterization of a more diverse group of prokaryotes using the sequence of multiple protein coding genes
What are the pros of using MLSA? Higher resolution Uses multiple genes Where 16S rRNA gene gives a genus classification, MLSA gives a species
What are the cons of using MLSA? Genes must be a single copy Must be present in all of the organisms being analysed
What are Ecotypes? Populations that are genetically cohesive and ecologically distinct
What classifications do the following analyses cover: 16S rRNA DDH Multilocus 16S rRNA - Family & Genus DDH - Genus, Species and Subspecies Multilocus - Species, Subspecies, Strain
What analysis method should be used for fine scale resolution? MLST(A)
Define metabolism The sum of all reactions that occur in a cell
What is a catabolic reaction? An energy-releasing metabolic reaction
What is an anabolic reaction? An energy-requiring metabolic reaction
Define macronutrients Nutrients required in large amounts (not associated with size of individual nutrients)
Define micronutrients Nutrients required in trace amount (not associated with size of individual nutrients)
Name 7 micronutrients (trace elements) needed by microorganisms Iron (Fe) Boron (B) Chromium (Cr) Copper (Cu) Manganese (Mn) Nickel (Ni) Zinc (Zn)
What is ' Free energy (G)'? Energy that is released that is available to do work
Define an exergonic reaction A reaction with a negative ∆Gº Bond is broken Energy released
Define an endergonic reaction A reaction with a positive ∆Gº Bond is formed Energy required
Is the substance that is oxidised in a redox reaction the electron donor or acceptor? Electron donor
Is the substance that is reduced in a redox reaction the electron donor or acceptor? Electron acceptor
What are the two classes of electron carriers? Prosthetic groups (attached to enzymes) Coenzymes (NAD+, NADH)
Energy released in redox reactions is stored in what three phosphorylated compounds? ATP Phosphoenolpyruvate Glucose-6-phosphate
What is the energy source for the following: Chemoorganotroph Chemolithotroph Phototroph Chemoorganotroph - organic molecules Chemolithotroph - inorganic molecules Phototroph - light
What is the carbon source for the following: Autotroph Heterotroph Autotroph - CO2 Heterotroph - organic molecules
What is the electron source for the following: Organotroph Lithotroph Organotroph - organic molecules Lithotroph - inorganic molecules
What form of respiration uses electron acceptors other than oxygen? Anaerobic respiration
Name four electron acceptors used in anaerobic respiration Nitrate (NO3-) Ferric iron (Fe3+) Sulfate (SO42-) Carbonate (CO32-)
What catabolic method uses inorganic chemicals as electron donors? Chemolithotrophy
Name four inorganic chemicals used as electron donors Hydrogen sulfide (H2S) Hydrogen gas (H2) Ferrous iron (Fe2+) Ammonia (NH3+)
Describe the characteristics of chemolithotrophy Uses inorganic molecules as electron donors Typically aerobic Begins with oxidation of inorganic donor Uses ETC and pmf (Autotrophic - uses CO2 as carbon source)
What organisms use ATP for assimilation of CO2 for biosynthesis? Photoautotrophs
What organisms use ATP for assimilation of organic carbon for biosynthesis? Photoheterotrophs
Briefly describe amino acid biosynthesis Carbon skeletons come from intermediates of glycolysis and citric acid cycle Ammonia is incorporated by glutamine dehydrogenase or glutamine synthesis Amino group transferred by transaminase and synthase
Molecular methods conclude that how much of all bacteria has been cultured? less than 0.1%
What are hypothetical proteins? proteins that likely exist but function is not presently known
Describe the pros of metagenomics (DNA from microbial community) Can detect genes that are not amplified by current PCR primers Powerful tool for assessing the phylogenic and metabolic diversity of an environment
Define Metagenome The total gene content of the organisms present in an environment
What is a Transcriptome? The entire complement of RNA produced under a given set of conditions (hybridisation techniques can be used in conjunction with genomic sequence data to measure expression)
What are Microarrays? Small solid-state supports to which genes or portions of genes are fixed and arranged spatially in a known pattern
Define Proteomics Genome-wide study of structure, function, regulation of an organism's proteins
Define Metabolomics The complete set of metabolic intermediates and other small molecules produced in an organism
What is one of the primary techniques for monitoring metabolites? Mass spectrometry
What is a Proteorhodopsin Light-activated retinal-containing proton pump found in many marine bacteria. These photoproteins are globally distributed in the ocean's photic zone and are capable of generating a proton motive force across the cell membrane.
How does 16S rRNA surveys differ from metagenomics? (Look at highlighted slide on L5)