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Biology Study Notes These are notes I took while studying, both from the course notes and some from the textbook.

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BIOL 240
Trevor Charles

Microbiology notes Why are bacteria important? Impact almost al bio in the world Influence the earths development Make up over 50 5 of the earths biomass Microbiology is the science of microorganisms (these are organisms that can only be seen with a microscope). Microbes(microorganisms) can be divided in to two Prokaryotes Eukaryotes bacteria Algae, fungi and protozoa Achaea Bacteria interact with different organisms e.g. root nodule in leguminous plants What makes a cell alive Cells have metabolism, this metabolism then results in growth, cells differentiate, they communicate, they are motile and they evolve Reasons for studying microbiology Microbes were the first life on earth Created the biosphere that allows macro organisms to evolve Multicellular organisms evolved from micro organisms Over 50% of the earths biomass Helps in the study of life Machine and coding functions of the cell Machine functions : energy production, metabolism, enzymes Coding functions: DNA replication and translation to form proteins These two functions are interrelated and they both result in growth Applications of microbiology Mining : can act on the ore of copper to release pure copper Agriculture: E.g., root nodules, plants that contain bacteria in their nodules do not need fertilizer Health and Medicine In animals cellulose digesting bacteria break down the grass in their bellies Food industries: production of cheese, wine, etc Bio fuels: corn to ethanol {good fuel} Bio remediation: using bacteria to clean up toxic pollutants or oil spills Biotechnology; production of drugs in pharmaceuticals. Better sanitation and the production of antibiotics helped reduce death caused by infectious diseases Where do microorganisms come from? Spontaneous generation was the first theory of microorganisms because of food spoilage. Louis Pasteur disproved the theory of spontaneous generation. With his experiment. Procedure Chicken broth was added to a flash with a long neck, the neck was stretched, and the broth was heated repeatedly and kept for a very long period there was no sign of microbes. Then after some time the flask is tipped so that the liquid touched the neck of the flask and then after some time the Broth spoiled Kochs postulates (germ theory of disease) Koch carried out an experiment to find out the causative agent of some diseases. Some diseased rats were tested and their blood had both red blood cells and bacterial cells this observations lead to: 1. The pathogenic organism should be present in all disease cases and absent from healthy animals 2. It should be able to grow in pure culture 3. The cells from the pure grown culture should be able to infect a healthy animal 4. If the blood is removed from the diseased animals, it should contain the same pathogen This lead to the following conclusions Specific organisms cause specific diseases; Kochs postulates can also be applied to other organisms Cell structure Prokaryotes do not have a nucleus DNA not surrounded by a nuclear membrane Eukaryotes DNA is in a nuclear membrane Also, have organelles that have their own DNA Are kimeric organisms and probably arose from an archaeal organism. Three domains of life Sequencing of the 16s (prokaryotes) or 18s (eukaryotes) ribosomal rna gene shows how closely related two organisms are. This is used to create the phylogenetic tree. The three domains of life are Bacteria Archaea Eukarya Physiological diversity of microorganisms for a cell to grow it has to take energy and carbon compounds from the environment. Two main source of energy are chemicals and light Chemotrophs get their carbon from chemicals e.g. chemorganotroph, chemolithotroph, and photo trophs Only archaeal are chemolithotrophs Heterotroph(humans require an external carbon source) and autotroph(plants make their own organic compounds) Most archaeal organisms are extremeophiles .Bio 140 notes two after mid term Terminologies in microbiology: Microbiologists are strict with their terminologies in order to distinguish between mutants, strains and mutations. The first organisms used to develop a genetic system were salmonella and e-coli. A mutant is a strain carrying a mutation A mutation is the change that occur within a gene to make another gene or allele This usually involves gain of function, loss of function, or change of function. Genotype is a description of all alleles within an organism, it is usually related to the wild type( the non mutated type) Phenotype of an organisms are the observable properties of the strain that contains the mutation - - - His(this is the phenotype) hisC or hisC ( and it is the genotype) The wild type of E-coli is K-12 Selectable phenotype: the bacteria can be placed in a medium so that only that phenotype can grow + in that medium. His is a selectable phenotype because they can grow in a medium that does not have histidine. His is a screen able phenotype, but it is extraneous. A selectable medium allows mutation that occurs in low frequency to be detected. Mutants arise spontaneously, mostly during replication. DNA polymerase is not a perfect enzyme. Replica plating is used to isolate mutants, this is done by treating the wild type strains with mutagens, this is plate is diluted and plated for single colonies and then it is grown on a complex medium; this plate is called the master plate. The master plate is then pressed on a sterile velvet placed on a wooden cylinder; this allows some cells to be transferred unto it. Some cells are transferred to a minimal medium and some are transferred to a complex medium. All the cells would grow in the complex media but not all of them would grow in the minimal media these are possible auxotrophs. replica plating Types of mutation: Auxotroph: cant produce a certain nutrient Non motile cant make their flagella Pigmentless: have diff colour from the wild type Temperature-sensitive: cannot grow at temperatures that usually support growth Silent mutation is a mutation that occurs at a DNA level but it does not affect the protein because different codons code for one amino acid, because the mutation is not shown in the amino acid. Nonsense mutation is when a mutation causes a stop codon, this results in transcription ending early resulting in an incomplete protein Missense when the mutation results in a different amino acid this might be beneficial or detrimental to the cell. Shifts in reading frame: a base can be substituted into the sequence it can be either removed or added to the reading frame. Depending on if a base has being added or removed it is called +1,-1 reading frame. If there is a mutation that occurs in the DNA binding region the effects are severe If there is a mutation that occurs in a region where the gene is not expressed the effects are not really felt. Mutagens; these cause mutation some increase the frequency of mutation Examples are base analogs they are very similar to the base and can be found in the DNA Examples of base analogs 5-bromo Uracil has the same structure as Thymine, it is supposed to bind with A but it binds very well with G Another analog is 2-aminopurine it looks like A but binds very well to C Also Radiation(ionisationradiation) is a mutagen it breaks up DNA into pieces There are also chemical mutagens; ultra violet light causes a dimer to form between the bases preventing the gene at that part to be read. Examples are nitrous acid; it deaminates A and C, hydroxylamine reacts with C The DNA has a high level of absorption when the wave length is 262nm SOS RESPONSE There are several genes in the cells whose expression are induced when DNA is damaged. UvrA is one of the genes and it is perfect. But sometimes the destruction can be so severe that the only way to fix the damage is to make errors. This is controlled by umuD. SOS is mediated by the lex a protein. When lex a is bound to the operator no transcription occurs. Derepression occurs when the damage lex A is inactivated, the rec A does the derepression by cleacing the lex A Ames test This is a test for mutagnecity if the product is mutagenic it might be carcinogenic. The test measures the frequency of the reversion on exposure to the chemical. The culture is placed in a perti dish and grown on a minimal medium Genetic recombination Recombination is an event that allows DNA molecules to be joined, homologous recombination occurs in eukaryotic organisms. It works the same for all organisms at a molecular level. It starts with a breakage in the DNA molecule then a single stranded molecule is made then Rec a binds to that molecula and makes it react with another molecule which is either complementary or similar. The DNA of the recipient that was where the new single strand is now is taken to the old DNA molecule that lost its single strand. This forms a HOLLIDAY junction it is like a cross between the two DNAs.
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