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Lecture 2

MBIO 1010 Lecture 2: Lecture 2

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MBIO 1010
Christopher Rathgeber

Microbiology 1010 – Lecture Notes Basic Steps Involved in Sequencing rRNA Genes Step 1: DNA is collected from a pure culture  Step 2: The SSU rRNA gene is amplified using the polymerase chain reaction (PCR) PCR – A technique used to synthesize many identical copies of a short sequence of DNA Step 3: The gene is sequenced  Step 4: Sequence is aligned with sequences from other organisms  Number of differences is used to calculate evolutionary distance Phylogenetic tree – A graphic representation of the evolutionary distance between organisms. The DNA itself is going to be quite large, you want to home into the area you are interested in. How you do is that is a primer who is sequence specific for that rRNA area. What happens, is you replicate just that segment. You have all of those copies and put to sequencing techniques so that we can know the nucleotide sequence. Then we do is we analyze them. Look for the highest degree of similarity to find relatedness. Molecular Phylogeny and the Tree of Life  Phylogenetic tree based on 16S or 18S ribosomal DNA sequences    All organisms can be grouped into 3 distinct domains of life: Bacteria, Archaea and Eukarya  Microorganisms are far more genetically diverse than plants and animals. 7 Microbiology 1010 – Lecture Notes 12.8 The Species Concept in Microbiology The species is the fundamental unit of biological diversity. But, what is a species? Phylogenetic Species Concept – “A group of strains that share certain diagnostic traits, are genetically cohesive and have a unique recent common ancestor” In practice, species of Bacteria and Archaea should have:  Most (but not all) characteristics in common o Greater than 97% sequence similarity in the 16S rRNA gene High degree of genome similarity    DNA-DNA hybridization  In the very near future: whole genome sequences? Phylogenetic species concept = It looks at the genetic similarities. If I take the sequence between the two bugs, 97% similarity otherwise they will be placed as different species. 12.10 Classification and Nomenclature Microbiologists use Hierarchical classification o Groups of organisms are placed in successively larger groups o In practice: Species, genus and phylum are commonly used. Domain is less specific. 8 Microbiology 1010 – Lecture Notes 12.10 Classification and Nomenclature Binomial species names Escherichia coli Genus (capitalized) Specific epithet (not capitalized)  Strains can be identified by symbols after the species name Ex. E. coli K12  Rules o Names are latinized. o Italicized or underlined. o Genus capitalized, epithet is not. o Genus name may be abbreviated the second time it’s used: E. coli. o Trivial names can be used, but do not follow these rules. The Discovery of Microorganisms Robert Hooke (1635–1703) The first to describe microbes   Used a compound micrscope – uses 2 lenses to magnify the image  Allowed magnfication up to 30x  Used it to observe:  Cells in cork Bread mold filaments – 1 microbe  Beginning of cell theory – all living things are composed of cells.  Antoni van Leeuwenhoek (1632–1723) Built microscopes that magnified specimen by 50-300x Observed single celled microorganisms – called them “animalcules”  First discovery of bacteria. This is the first bacterium/prokaryote to be seen 9 Microbiology 1010 – Lecture Notes Pasteur and Spontaneous Generation Louis Pasteur (1822–1895) o Studied wine and beer production Yeasts convert sugar to alcohol in the absence of oxygen  Fermentation – “La vie sans air”  life without air o  Bacteria can sour wine by converting alcohols to acid o Developed a method of gentle heating to kill unwanted bacteria – Pasteurization Lactic acid makes it taste sour. Pasteurization = It does not destroy all microbes (it decreases the microbial count) so you have a longer shelf life  Prepared meat infusions inside of long swan-necked flasks 
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