MICROBIAL DIV EVOL
MICROBIAL DIV EVOL MIBO 4300
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Dr. Jayda Mayert
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This 7 page Study Guide was uploaded by Dr. Jayda Mayert on Saturday September 12, 2015. The Study Guide belongs to MIBO 4300 at University of Georgia taught by Staff in Fall. Since its upload, it has received 74 views. For similar materials see /class/202391/mibo-4300-university-of-georgia in Microbiology at University of Georgia.
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Date Created: 09/12/15
Study guide 1 Prokaryotic diversity and natural populations 1 Where are most of the earth s prokaryotes found 2 How does the abundance of prokaryotes compare to that of plants and or animals 1 Describe the principles of mass spectroscopy 2 What is isotope fractionation Given the ratio of 13C C in a sample and the PDD standard calculate the dell3C Ifthe dell3C is very low the material is enriched in 13C or 12 5 Describe a consensus model for the early evolution of prokaryotic life If this model is correct what are the implications for the evolution of eukaryotes 5 Describe the different types of diversity What practical problems can be solved by studying prokaryotic diversity Describe how numerical taxonomy is performed Describe how DNA hybridization is performed Describe the advantages and limitations of numerical taxonomy Compare different types of diversity between prokarotic and eukaryotic taxa Given a phylogenetic tree determine the similarity or difference between any two taxa What taxonomic ranks are widely used in bacteriology Describe how multilocus enzyme electrophoresis is performed In your description be sure to include how one might lyse the cells and the role of PMS and MTT Given a list of electrophoretic types for a number of strains like Table 9 in your handout be able to construct a dendrogram like Figure 2 on the same page of your handout What is the clonal model for the population structure of prokaryotic species Is this model applicable to all prokaryotic species What is the Index of Association and why is it used Be able to discuss the question of whether or not prokaryotic species exist in nature Be able to describe how PCR amplification of genes from the environment is used to learn the nature of prokaryotic communities Describe some potential errors or artifacts that can occur when studying the distribution of 168 rRNA or other genes in environmental DNA Include in your answer descriptions of chimeras affect of gene composition such as high mol GC heteroduplexes in PCR of closely related templates and heterogeneity within a single organism Describe how FISH might be used to identify organisms in natural samples For soil compare the differences in the number of prokaryotes observed by microscopic and culture techniques Why are these values different What about the gastrointestinal tract of humans Why are the cell number observed and the CFUs different 21 Compare the microbial diversity in soil the gastrointestinal tract and subgingival plague 12 509080 Nt O LA HHH H gt19 A 00 ND I 050 Define distinquish andor describe the following terms isotope fractionation taxon stromatolites phylogeny microfossils numerical taxonomy RNA world unit character banded iron formations hypothetical median organism endosymbiosis species prokaryotes and eukaryotes systematics phase variation taxonomy genospecies classification DNA hybridization natural classification Tm identification delta Tm GC ratio or mol GC MLST FAME analysis Indel polyphasic taxonomy speci c epithet type strain neotype strain Approved List Validation List Bacteriological Code Bergey s Manual ICSP IUMS IJSEM homology orthology paralogy multilocus enzyme electrophoresis allozyme activity stain population clone Some general questions recombination Index of Association gene tree organismal tree PCR Cot curve molecular chronometer chimera DAPI FISH enrichment culture Microelectrode Viability staining Wino gradsky column Metagenome 1 Why is the abundance of prokaryotes or any other group of living organisms important 2 Eukaryotes appeared to have arisen 1520 Gy ago at a time when prokaryotes were already a major component of the biosphere What are the implications of this observation on the nature of the eukaryote s 3 Given some objects be able to determine their similarity using a numerical scheme 4 If prokaryotes are clonal with little exchange of genetic information within the population why do we observe large groups of phenotypically similar and genetically related strains 5 Compare what can be learned by communities of prokaryotes I I for studying natural 6 In soil and many other environments only a small fraction typically 15 of the cells observed microscopically can be cultivated in laboratory medium Why 7 How might one characterize the organisms in some of these unclassi ed groups that have only been detected by rRNA gene sequencing Study guide 2 Additional Resources Readings from Madigan and Martinko 2006 Biology of Microorganisms pp 101132 331350 531556 577592 and Al For Al the appendix on thermodynamics be familiar enough with this section so that you could make calculations similar to those in the lectures and answer questions based upon these calculations Readings from Staley et al 2007 Microbial Life Chapters 6 8 9 and 21 The Prokaryotes vol 1 chapter 2 Stackebrandt General nutrition and respiration De ne distinquish andor describe the following terms siderophore Aw micronutrient ApH growth factor avoprotein enzyme cytochrome catalyst nonheme ironprotein NADNADH cycling ferredoxin fermentation quinine respiration proton motive force oxidative phosphorylation Complexes 1 II III IV photophosphorylation ATPase ATP synthase NADH dehydrogenase PMF citric acid cycle glycolysis gluconeogenesis 1 What is the elemental composition of the cell and what are the sources of these elements 2 How do enzymes catalyze reactions 3 Why are ATP and acetylcoenzyme A considered energyrich compounds What are some other energy rich compounds 4 Compare the ways that prokaryotic cells generate a PMF by respiration photosynthesis and fermentation 5 How is respiration coupled to biological work Be able to describe the electron transport chain in Paracoccus from the oxidation of NADH to the reduction of O2 6 What is the AG and why is it important Given the PMF or the midpoint potentials of the some electron donors and acceptors calculate the AG 7 From Table Al2 given in class identify potential electron donors and acceptors that might support the growth of prokaryotes Include possible components of the electron transport chain that could serve as intermediates 8 Compare the midpoint potentials for various electron donors for aerobes How does the midpoint potential affects the energy available for growth and the pathway of NAD reduction Photosynthesis 1 In general terms what types of diversity are found in prokaryotic photosynthesis compared to the chloroplast Include in your answer a comparison of the phylogeny of photosynthetic prokaryotes types of reaction centers and light harvesting complexes types of electron transport chains types of internal membranes and types of electron donors 2 What are the major types of pigments in photosynthetic organisms Why do organisms have different pigments What is the difference between light harvesting and reaction center chlorphorylls 3 How do photosynthetic bacteria purple vs green form NADPH Why do they need NADPH anyway 4 Compare the distribution in nature of the photosynthetic bacteria and the cyanobacteria Be able to describe a major ecological function or role of a member of each group 5 Describe the chlorosome 6 Describe a symbiosis that is common with members of the Chlorobiaceae and some unidentified rodshaped cells 7 Describe the major types of organisms related to the cyanobacterial lineage 8 What types of cellular differentiation occur in the cyanobacteria What types of developmental cycles occur 9 Don39t worry about knowing the taxonomic scheme for the cyanobacteria if you can answer questions 7 and 8 10 Compare the roles of prokaryotes and eukaryotes in the total productivity of the ocean Where are the marine phototrophs found in the ocean 11 Describe nitrogenase and the energy requirements for N2 fixation 12 Describe the heterocyst How does it protect nitrogenase from 02 How are nitrogenous compounds transported between the heterocysts and vegetative cells 13 How do the marine cyanobacteria protect nitrogenase from 02 De ne distinquish andor describe the following terms cyanobacteria prochloron cyanelle phycobilin phycobilisome phycobiliproteins thylakoid tetrapyrrole chlorophyll reaction center light harvesting pigments budding multiple ssion baeocytes trichome hormogonia purple nonsulfur bacteria purple sulfur bacteria anoxygenic photosynthesis oxygenic photosynthesis photoheterotroph reverse electron transport chlorosome chemocline gas vesicles bacteriorhodopsin halorhodopsin slow rhodopsin haloarchaea akinete Synechococcus Prochlorococcus picoeukaryotes nitrogenase FeMoCo alternative nitrogenase microplasmodesmata glutamine synthase heterocyst gas vesicle glutamate synthase diurnal cycle oxidase purple bacteria Study guide sulfur oxidizers methane oxidizers nitrifiers 1 Compare the habitats of Thiovulum Beggiatoa and Thioploca How has each organism specialized for its habitat 2 Describe the sulfur cycle and the role of each of the microbial groups within the cycle 2a What chemical transformations are typical of the sulfur oxidizing prokaryotes Why are many of these organisms acidophiles 2b Given the molecular formula of a sulfur nitrogen or carbon containing compound calculate the oxidation state of the sulfur nitrogen or carbon atom see pp A12 3 Are the sulfuroxidizing bacteria a monophyletic group Explain some of the diversity 4 How does Thiovulum form veils Why do you suppose it does so Compare chemotaxis in Thiovulum to that common in other prokaryotes ie E coli 7 How does pH affect the free energy available for the ironoxidizing bacteria Explain the chemical rationale 8 Why are the growth yields so poor for the ironoxidizing bacteria Are these guys very efficient ie do they get most of the energy available from that reaction 9 How is Thiobacillusferrooxidans used in mining low quality ores Describe some processes utilized to mine copper gold and uranium 10 What is the major geochemical role of the methaneoxidizing bacteria Why is it important to studies of the greenhouse effect 11 Compare the soluble and particular methane monooxygenase of methylotrophic bacteria 12 What are the other common substrates of the methylotrophs 13 Compare the serine ribulose monophosphate and pterin pathways of formaldehyde assimilation Know the unique steps the amount of ATP required C1 assimilated and possible physiological differences How might the RuMP pathway be used to make pentoses 14 Compare Type 1 Type II and Type X methylotrophs 15 Describe some symbiosis of methylotrophs with plants and animals 16 How are methylotrophs used to treat groundwater 17 Describe the nitrogen cycle on earth including the microbial groups important at each step and the oxidation state of N 18 What are the major phylogenetic groups of nitrifying bacteria What about the anaerobic nitrifying bacteria 19 Compare the energetics of ammonia and nitrite oxidation How do nitrifying bacteria reduce NAD 20 What are three rationales for the poor growth of the nitrifying bacteria 21 How much nitrite must be oxidized to reduce NAD Why is so much required 22 Where is the Anammox reaction found Be able to describe the pathway of ammonia oxidation the electron donor and electron acceptor Define distinquish andor describe the following terms specialist acidophile generalist mesophile mixotrophic thermophile chemolithoheterotroph veils obligate chemolithotroph chemotactic neutrophile oligotroph microaerophile rusticyanin initiator reaction propagation cycle greenhouse gas methanotroph methylotroph onecarbon compound halomethane methylamine methane methanol formaldehyde formate pMMO sMMO serine pathway RuMP pathway hexulose6phosphate synthase hexulose phosphate isomerase serine hydroxymethyl transferase hydroxypyruvate reductase malate thiokinase malyl coenzyme A lyase glyoxylate bypass Oz phobic tetrahydrofolate tetrahydromethanopterin trichloroethene nitri cation nitrogen cylce nitric oxide nitrous oxide nitrate nitrite ammonia nitrifying bacteria ammoniaoxidizing bacteria Nitrospz39ra ammonia monooxygenase hydroxylamine oxidoreductase nitriteoxidizing bacteria nitrite oxidoreductase Ks Anammox candidatus 1 39 I c I 39 1 J
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