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Microbiology Chapter 3 and 12 lecture notes

by: Andie Gargiulo

Microbiology Chapter 3 and 12 lecture notes Bio 380

Marketplace > James Madison University > Biology > Bio 380 > Microbiology Chapter 3 and 12 lecture notes
Andie Gargiulo
GPA 3.2
Pradeep Vasudevan

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About this Document

These are the filled in lecture notes from Dr. Pradeep's class. Also included is drawn out pictures of important topics throughout the chapter
Pradeep Vasudevan
Class Notes
Microbiology, Chapter 3 & 12
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This 13 page Class Notes was uploaded by Andie Gargiulo on Wednesday October 7, 2015. The Class Notes belongs to Bio 380 at James Madison University taught by Pradeep Vasudevan in Fall 2015. Since its upload, it has received 43 views. For similar materials see Microbiology in Biology at James Madison University.


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Date Created: 10/07/15
Microbiology Lecture Notes Chapter 12 Microbial Evolution and Systematics Formation and Early History of Earth Earth 45 billion years old Sedimentary rocks date to 386 billion years old Early Earth was m no oxygen and much hotter First biochemical compounds were made by M not derived from life or sterile systems set the stage for origin of life Origin of Cellular Life Subsurface origin hypothesis 9 life originated at hydrothermal springs on ocean oor because conditions would have been less hostile and more stable compared to surface Also steady and abundant supply of energy may have been available RNA Proteins DNA RNAbased RNA world theory9 rst selfreplicating systems RNA can bind small molecules and has catalytic activity may have catalyzed its own synthesis Proteins replace RNA as catalysts DNA more stable replaces coding function of RNA Buildup of lipids 9 synthesis of phospholipid membrane that enclosed the cell s biochemical and replication machinery LUCA9 last common universal ancestor where divergence into Bacteria and Archaea begins Early Metabolism Energygenerating metabolism Exclusively anerobic absence of free oxygen and chemolithotrophic Obtained carbon from 2 autotrophs Obtained energy from Hg Ancestors of Bacteria and Archaea diverged 37 billion years ago Stromatolites 9 fossilized microbial mat of lamentous prokaryotes and trapped sediment found in rock 35 billion years old or younger Oxidation of Earth Early forms of photosynthesis 9 anoxygenic releases sulfur from H28 instead of 02 from water Cyanobacteria rst appeared 27 billion years ago use HzO instead of H28 generating 02 Oxygen could not accumulate as atmospheric 02 because abundant reduced iron present Great Oxidation Event9 started oxidizing iron to iron oxide black evidence of banded iron formations on sedimentary rocks Oxygenation and Ozone Shield Once all iron was consumed 02 accumulated 9 atmosphere went from anoxic to oxic Oxygen now available as an electron acceptor 9 more energy and nutrient absorption Formation of ozone layer 9 protect from UV rays Eukaryotic Evolution Oxygen spurred evolution of organellecontaining eukaryotic microorganisms Unicellular eukaryotes arose on Earth about 2 billion years ago Endosymbiosis9 Supported hypothesis for origin of eukaryotic cells larger cells engulfed smaller cells Symbiont 9 respiring bacteria Ex mitochondria Symbiont 9 oxygen cyanobacterium Ex chloroplasts Evidences for Endosymbiosis Mitochondria and chloroplasts have small circular pieces of DNA Chloroplast and mitochondrial ribosomes and 168 RNA sequences are closely related to bacteria Eukaryotic organellar ribosomes are inhibited by antibiotics that inhibit bacteria Chimeric Nature of Eukaryote 9 attributes to both Bacteria and Archaea Lipi of the type found in bacteria the ester linkages Transcription and translation systems more similar to archaea Two hypotheses to explain formation of the eukaryotic cell 1 9 Eukaryotes began with a nucleus and later acquired mitochondria and chloroplasts by endosymbiosis Not well accepted because nucleus membrane lipids similar to that of bacteria 29 Hydrogen Hypothesis Eukaryotic cell arose from association between a H2 producing or respiring bacterium the symbiont and an archaeal host Engulfment happened rst and then the formation of the nucleus after genes for lipid synthesis were transferred Chloroplasts happened later Phylogeny The evolutionary history of a group of organisms Haeckel s Tree of Life 1866 9 had aws Whittaker s Tree of Life 1869 9 ve kingdom classi cation Now inferred indirectly nucleotide sequence data Carl Woese created the use of rRNA for phylogentic studies in 1970 s Established the presence of three domains of life Bacteria Eukarya and Archaea This A is not a very old discovery RECAP9 Different types of RNA rRNAribosomal mRNAmessenger tRNAtransfer rRNA Ribosomes are made up of two subunits Eukaryotes 9 408 and 608 SOS Prokaryotes9 308 and SOS 708 S Svedberg units sedimentation coef cients when subjects to centrifugal force 308 and 408 subunits also called small subunits SSU Contains bacteria and amp eukarya rRNA Most widely used genes in phylogenetic analysis Found in all domains of life Functionally constant Suf ciently conserved slowly changed Suf cient length Comparative rRNA sequencing Ampli cation of the GENE encoding SSu rRNA PCR Sequence analysis 9 align sequence of interest with sequences from homologous same position genes from other strains or species Phylogenetic tree9 illustration of relationship among sequence Branch length represents number of changes that have occurred along that branch Universal phylogenetic tree Domain Bacteria 9 80 major phyla Domain Archaea 9 seven major phyla Domain Eukarya 9 eukaryotic organelles originated Within Bacteria Evolutionary Analysis Ribosomal Database Project RDP 9 a large collection of rRNA sequences BLAST Basic Local Alignment Search Tool 9 aligns query sequences with those in GenBank Microbial Evolution Evolution 9 the change in allelic frequencies over time Allele 9 alternate version of a gene Mutations 9 random changes in nucleotide sequence on the genome Can occur due to errors in replication UV radiation etc Recombination9 exchange of DNA between genetic elements Homologous or nonhomologous Evolutionary Process Selection 9 based on tness or the ability to produce viable progeny and contribute to genetic makeup of future generations Neutral mutations no effect Deleterious mutations decrease tness Bene cial mutations increase tness Genetic drift 9 random process that can cause gene frequencies to change over time evolution Evolution in the absence of natural selection Species concept in Microbiology Prokaryotes are haploid and do not undergo sexual reproduction Phylogenetic Species concept 9 collection of strains sharing a high degree of similarity in several independent traits 97 or greater 16S rRNA gene sequence identity Considered a new species if 16S rRNA gene sequence differs by more than from any named strain New gw if differs by more than 70 or greater DNADNA hybridization 9 genomes of two organisms are hybridized Proportion of similarities in the gene sequence observed 70 or higher suggest strains belong to the same species Less 25 suggest genus Microbial Systematics Systematic 9 studies of the diversity of organisms and their relationships Links phylogeny with taxonomy Taxonomy 9 science of biological classi cations Identi cation 9 determining that a particular isolate belongs to recognized taxon Classi cation 9 arrangement into group Nomenclature 9 assignment of names to taxonomic groups Taxonomic Methods Polyphasic approach 9 genotypic and phenotypic Multilocus many genes sequence typing MLST 9 a method in which several different housekeeping genes are sequenced and the sequences are used to distinguish the organisms Housekeeping genes encode essential functions in cells and are always located on the chromosome rather than the plasmid Ribotyping 9 analyze DNA fragments generated from restriction enzyme digestion of genes encoding SSU rRNA Taxonomic Methods Phenotypic Analysis 9 examines the morphological metabolic physiological and chemical characters of the cell Variation in type and proportion of fatty acids present in the membrane lipid Fatty acid analysis FAME fatty acid methyl ester This would not work with Archaea because they lack true fatty acids Require rigid standardization 9 because of variation in function of temperature growth phase and growth medium Classification and Nomenclature Classi cation 9 organization of organisms into progressively more inclusive groups on the basis of either phenotypic similarity or evolutionary relationship Species Genus Family Order Class Phylum Domain Nomenclature 9 given descriptive genus names and species epithets following the binomial system of nomenclature Regulated by the International Code of Nomenclature of Bacteria Microbiology Lecture Notes Part 2 Chapter 3 Microbial Metabolism Cell Chemistry and Nutrition Nutrient9 supply of monomers required for growth Macronutrients9 nutrients required in large amounts 95 dry weight Dry weight is after you have dried out all of the water Micronutrients 9 nutrients required in small amounts Ex Trace Elements Co Cu Fe Mn Ni Zn amp Growth factors Carbon 0 REQUIRED BY ALL CELLS Typical bacterial cell 50 carbon dry weight Maj or element in ALL classes of macromolecules Source Autotrophs 9 inorganic carbon C02 and Heterotrophs9 organic carbon Nitrogen Typical bacterial cell l3 nitrogen Maj or component of proteins and nucleic acids Organic form 9 amino acids amp inorganic from 9 nitrates and ammonia N2 from atmosphere 9 Nitrogen xing bacteria Other nutrients Phosphorus P 9 synthesis of nucleic acids and phospholipids Sulfur S 9 Vitamins thiamine biotin lipoic acid and coenzyme A Sulfurcontaining amino acids 9 cysteine and methionine Magnesium Mg 9 stabilizes ribosomes membranes and nucleic acids Required for many enzymes nutrients Iron 9 cellular respiration Key component of proteins involved in electron transport cytochromes Anoxic condition 9 ferrous Fe 2 form soluble Oxic condition9 ferric Fe3 form insoluble Siderophores9 iron binding agents Used to obtain iron from insoluble mineral form Ex derivatives of hydroxamic acid Growth factors 9 organic micronutrients Vitamins 9 most commonly required growth factors and function as co enzymes Also amino acids purines and pyrimidines Microorganisms can synthesize almost all of these compounds some must be provide in the medium Culture Media Solids or liquids used in growth transport and storage of microorganisms Two classes Defined media 9 precise chemical composition is known Complex media 9 composed of digests of chemically undefined substances EX yeast and meat extracts Defined Media Made using precise amounts of highly puri ed organic or inorganic compounds Exact chemical composition is known Complex Media At least one ingredient that is not chemically m unde ned Exact composition and amounts of carbon nitrogen etc are unknown Usually enzymatic digests of animals plants or microbes Casein milk protein peptone soybean gelatin and yeast extract yeast cells Highly nutritious Selective Media Contain agents that growth of able to grow microorganisms but not others Selects for microbes that are able to grow in presence of the inhibitor Ex Mannitol salt agar Differential Media Contains an indicator Allow differentiation of chemical reactions Media changes colors or there is formation of gas bubbles or precipitates Most if not all differential media are also selective Lamp El In Jail Half X I u a J r J 11 n x w 39 Ll 1 3 i I Ir 4 r l Law 5 I r KR a a I rx ml hall 1 I ili w A y I w 1 5 m E a p i 1 T u 1 I u M q 7 r I 1 Wu vku A 9 l m n u A V I x LE a r 1 r nay V 7 a 1 a a H W JL L 111 L h In I l 1 a 1 ITI 3 fr l H NW1 1 l 2 559 L n a i a i r uull m I l J 1II If u 1 i h u k1 m If 1 NI x uku lL in f I 1 WI I I 1 I L a n In 391 III an 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