Lecture 2 - Basics and Phylogeny.pdf

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Cell and Systems Biology
William Navarre

MGY377H © Lisa | Page 13 L E C T U R E 2 : B A S I C S A N D P H Y L O G E N Y BACTERIA VS. VIRUSES  viruses: microscopic, not cellular  viruses are essentially nucleic acid (DNA/RNA)wrapped in a protein or lipid/protein coat  they don’t have a metabolism per se: they require the help of cells to replicate their genomes & make progeny  bacteria: microscopic, cellular organisms, single cells or cell clusters BACTERIA ARE SINGLE-CELLED ORGANISMS 1. they have a metabolism  bacteria take up chemicals from the envmt & convert them into biomass/NRG  they excrete waste products  bacterial cells contain lipids, proteins, sugars, & nucleic acids (DNA & RNA) 2. they reproduce autonomously  bacteria take simple chemicals from the envmt to generate more complex ones that are used to create new cells under the direction of genetic info contained w/in the pre-existing cells 3. they can differentiate  many bacteria can generate new cells that are strikingly different than the parental cell 4. they can communicate & coordinate w one another  most bacteria can communicate by means of chemical signalling (quorum sensing) 5. they can move autonomously  many bacteria possess flagella or other cell structures to help them move 6. they can sense their envmt & respond either directly or by changing the genes they express (stress response) 7. they can evolve (so do viruses)  bacteria can change over time to both gain new properties & lose old ones PROKARYOTES VS. EUKARYOTES  prokaryotes (prokaryotic cells): cells that lack a true membrane-enclosed nucleus  bacteria & archaea (archaeobacteria) are prokaryotes & have their genetic material located in a nucleoid  a bacterial cell has o cytoplasm surrounded by a single envelope (cytoplasm contains DNA in nucleoid) o envelope has lipid membrane boundary (& structural cell wall)  eukaryotes (eukaryotic cells): cells that have a membrane-enclosed nucleus  algae, fungi, protozoa, plants, & animals are all eukaryotes  bacteria & archaea are usually smaller than eukaryotic cells 1. eukaryotic cells have a variety of complex membranous organelles in the cytoplasmic matrix each of which has a distinctive structure directly related to specific fxs 2. the genomes of eukaryotic cells are contained w/in a membrane-enclosed nucleus 3. in contrast, the cytoplasmic matrix of prokaryotes typically contains constitutes that are not membrane- enclosed 4. biochemical processes that normally occur in a chloroplast/mitochondria of eukaryotes will take place in the membrane/cytoplasm of prokaryotes MGY377H © Lisa| Page 213 5. prokaryotes are simpler functionally than eukaryotes in several ways: they lack mitosis & meiosis and are not capable of phagocytosis & intracellular digestion  prokaryotes are LESS COMPLEX than eukaryotes (but not less evolved) Structure property Prokaryotes Eukaryotes Genetic materials Nucleoid (no membrane) Nucleus (membrane-bound) Mitochondria (energy production) Absent Present (in most) Chloroplasts (photosynthesis) Absent Present (in some) Golgi apparatus (packaging and secretion) Absent Present Endoplasmic reticulum (protein and lipid Absent Present synthesis) Lysosome (intracellular digestion) Absent Present TAXONOMY  taxonomy: the science of biological classification  classification: arrangement of organisms into groups (taxa)  nomenclature: assignment of names  identification: determining to which recognized taxon any given bacterial isolate belongs  phylogeny analysis: classification based on evolutionary relationships (w/in prokaryotes and bw prokaryotes & eukaryotes)  significance:  allows to organize huge amount of knowledge about organisms bc all members of a particular group share many characteristics  allows to make predictions for further research based on knowledge of similar organisms  allows to communicate efficiently in the scientific community  essential for accurate identification of microorganisms  taxonomic ranks (hierarchy): domains (new)/kingdoms (old), phylum, class, order, family, genus, species  genus: a collection of species  species: a collection of strains that share many stable properties & differ significantly from other groups of strains  bacterial strain: populations of organisms that descended from a single org or pure culture isolate that differ from one another in only small & subtle ways  binomial system of nomenclature: a system of taxonomy dvlped by Linnaeus in the early 18 th century  each species receives a 2-term name (genus, species)  the naming of species & other taxa follows a set of rules: the International Code of Botanical Nomenclature (ICBN)  Bergy’s Manual of Systematic Bacteriology: describes the major properties of all known prokaryotes, both Bacteria & Archaea CLASSIFICATION SYSTEMS  bacteria species are hard to classify; classification rules for animals are hard to apply to bacteria  phonetic classification: classification based on phenotypic characteristics may reveal possible evolutionary relationships  morphological characteristics (cell shape/size, colonial morphology, ultrastructural characteristics, staining behaviour, cilia & flagella, mechanisms of motility, endospore shape & location, spore morphology & location, cellular inclusions, colour) MGY377H © Lisa| Page 313  physiological & metabolic characteristics (C & N sources, cell wall constituents, NRG sources, fermentation products, general nutritional type, growth temp optimum & range, mechanisms of NRG conversion, motility, O2relationships, pH optimum & growth range, photosynthetic pigments, salt requirements & toleran
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