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Microbiology test 3 week 1

by: UNT_Scientist

Microbiology test 3 week 1 Biol 2041

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About this Document

These are the notes for the third test. This is just for the first week, therefore it includes the notes from good friday.
Daniel Kunz
Class Notes
Microbiology, kunz
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This 14 page Class Notes was uploaded by UNT_Scientist on Saturday March 26, 2016. The Class Notes belongs to Biol 2041 at University of North Texas taught by Daniel Kunz in Winter 2016. Since its upload, it has received 57 views. For similar materials see Microbiology in Biology at University of North Texas.


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Date Created: 03/26/16
Week 1 test 3   Microbiology   ● Chemical methods   ○ Disinfectants and antiseptics   ■ Phenolics­ P  ● Example   ○ Lysol   ● Biphenyls, hexachlorophene, triclosan (found in antibacterial soap)  ○ Disrupt plasma membrane   ○ Once there is a triclosan resistance   ■ There is a resistance in ampicillin, tetracycline etc.   ■ Triclosan is the third most found thing in  waterways.   ■ It is hard to degrade Sweden has discontinue use.  ● Instead use ethanol   ■ Halogens ­ H  ■ Alcohols ­ A  ■ Strong oxidants­ O  ■ Heavy metals ­HM  ■ Quats­Q­detergent like   ● Are an ammonium in with a Benzalkonium Chloride. This is sued  to clean dairy equipment  ○   ○ First table “ HM HM H A Q O  ○ Third table    ○ Fourth table    ○ Resistance (high to low )   ■ Prion   ■ Endospore of bacteria   ■ Mycobacteria   ■ Cysts of Protozoa   ■ Vegetative Protozoa   ■ Gram negative bacteria   ■ Fungi   ■ Virus with envelopes  ■ Gram posits  ■ Virus without envelopes   ○ Drugs   ■ 1928  ● Fleming discovered penicillin   ■ 1940   ● H. Florey and E. Chain performed first clinical trials  ■ Table 20.1  ● 20.2  ■ Broad spectrum antibiotics   ● Works on a lot of organisms   ○ Example   ■ Streptomycin   ● Antibiotic   ● Protein synthesis   ■ Tetracycline  ● Antibiotic   ● Protein synthesis    ■ Narrow spectrum antibiotics  ● Works on some organisms   ○ Example  ■ Penicillin   ● Antibiotic   ● Works on gram positive bacteria in cell wall   ● Many organisms are resistant to this   ■ Ketoconazole   ● Not antibiotics   ● Fungi membrane disruptions  ■ Acyclovir   ● Not antibiotic   ● Replication   ■ Isoniazid   ● Cell wall   ● Not antibiotic   ■ Antiviral drug  ● Nucleoside and nucleotide analgesic  ○ the virus can't tell the difference and it inhibits replication   ● Applied and industrial Microbiology chapter 28   ○ Packaging   ■ Dairy products   ● Most involvedactic acid bacteria   ● Cheese   ○ Hard cheese produced by actic acid bacteria   ■   ● Yogurt  ○ Lactobacillus Acidophilus   ■   ■ Beverages   ● Yeast fermentations   ○ Saccharomyces cerevisiae  ○ Saccharomyces carlsbergensis   ■ some of the first brewery started by Carl Berg  ● strain 1 v strain 2   ○ same species just different at the  genetic level    ○ this is responsible for the different  taste of each beer  ○ Beer   ○ Wine   ■ Fermentable sugar   ● sugars that can be anaerobically broken  down   ■ Non­beverages   ● Sauerkraut   ○ Lactic Acid Bacteria   ● Soy sauce   ○ Aspergillus   ● Olives   ○ Lactic Acid Bacteria   ■ Bread   ● Yeast ­­> ethanol + C2   ● sourdough rye  ○ Lactic acid bacteimpart flavor   ■ Cured meat  ○ Lactic Acid Bacteria   ■ aka LABs  ■ Non spore forming   ■ Gram positive rods   ○ Industrial microbiology   ■ Solvents   ● Acetone   ○ Clostridium   ● Ethanol   ○ Bacterial Fermentation   ■ Food supplements  ● Amino acids  ○ phenylalanine +aspartate =Aspartame [Nutrasweet]  ● Citric acid   ○ Aspergillus  ● Vitamins   ○ B12   ○ Riboflavin   ● Enzymes   ○ Amylases   ○ Proteases   ■ Breaks down proteins into amino acids   ■ Bacillus   ● Acts extracellularly   ○ Results in zones of clearing when  placed on a plate   ■ Aspergillus  ● Antibiotics  ● Biomedical products   ○ Anticancer compounds  ○ Anti­clotting factors   ○ Vaccines   ● Fermentations on the industrial size   ○ fig 28.10   ○ Uses steam for sterilization   ○ Is constantly feeding liquids through   ■ Chemostat  ● We never have to stop this reaction   ○ Primary fermentation   ■   ■ product is made in t Trophophase   ○ secondary fermentation   ■ this is common for any antibiotic   ■   ● Product is made in thdiophase   ○ Biotransformation   ■ Use of microbes and enzymes in pharmaceuticals  to change an organism via a biological process to  makes sure it is stereospecific   ○ Biotechnology   ● Results of manipulation of microorganisms  ○ Production of Rennin is found in young calf now we  genetically engineered   ○ Production of insulin is found in horses now is genetically  engenered   ● Environmental microbiology Chapter 27  ○ Habitats   ■ Microbial communities resulting in metabolic diversity   ● Soil   ○ The deeper in the soil we go the less organisms measured   ■ Low surface organisms are chemolithotrophs   ■ High surface organisms are chemoorganotrophs   ○ Rhizosphere (mycorrhizal)  ■ responsible for the growth of plants   ● Water   ● Air   ○ Not conducive to microbial growth   ○ Usually fungal spores  ○ Environmental Balance   ■ Microbial biogeochemical cycles   ○ Microbial activities that contribute to environmental balance   ■ Biodegradation  ● fig 27.8   ● 2,4 ­D   ○ 2,4­Dichlorophenoxyacetic Acid  ○ Degrades over time   ○ How organisms make a living off of this chemical  ■ 2,4­D, NH​, Sulfur, Phosphorus, Trace metals   3​ ● 2,4,5­T  ○ 2,4,5­ trichlorophenoxyacetic acid   ○ Doesn’t degrade   ○ More recalcitrant    ■ Harder to degrade  ● How herbicides go away  ■ Bioremediation   ● Clean up a contaminated area   ● Enhanced by nitrogen and phosphorus fertilizer  ■ Bioaugmentation   ● Addition of microbes to degrade pollutant   ■ Wastewater treatment   ■ Solid waste composting   ○ Water quality   ■ Chemical contamination   ● Organic materials (pesticides, agricultural runoff) and inorganic  materials  (mercury, excess nitrates, fluorides, led)  ■ Leads to the transmission of infectious disease    ■ Microbial contamination   ● Coliforms, viruses and protozoa (cyst and cryptosporidium)   ○ What is a coliform?:  ■ Gram negative bacteria that arise from the  mammalian colon   ■ If found in water there is a fecal contamination of  the water.   ■ Is tested by the presenceE.coli   ■ 1 colony per every 100 ml is a satisfactory test  ■ 2­22 colonies per every 100 ml is unsatisfactory  ■ Filtered and then smeared over EMB  (differential/  selective material)  ○ The carbon cycle   ■   ○ Nitrogen cycle  ■   ● Ammonification   ○ Protein​go through a process of hydrolysis and become  ammonia   ● Nitrogen fixation   ○ Takes ​itrogen gand makes iammonia   ● Nitrification   ○ Conversion o​mmonia to anitr and takes th​itr​and  makes itnitrate   ● Denitrification  ○ Takes a​itrat and makes it i​itr​ The​itr is  converted t​itric oxand finally i​itrogen gas   ○ Occurs when the soil becomes anaerobic  ○ Caused by denitrifying bacteria   ● Plants prefer nitrates   ○ We till gardens and fields to increase the presence of  nitrates with the unitrobacter  ●   ○ Food pyramid   ■ Primary producers (at the bottom aka the biggest part of the food  pyramid)  ● Photosynthetic and chemosynthetic organisms   ● Need lots of these to feed small amounts of Quaternary  consumers   ■ Secondary consumers   ■ Tertiary consumer   ■ Quaternary consumers  ● Smallest part of food pyramid   ● Example   ○   ■    ● Genetics  ○ Two hallmarks of biology:   ■ energy transformation   ■ Information flow   ○ Chromosomes  ■ Physical structures carrying hereditary information   ○ Gene   ■ DNA segment encoding a​unctional produ​eg  prote)   ■ What genes are, how I for carried, how I for expressed, how genes  replicated how genes transferred?  ○ Central dogma   ■ DNA ­­transcription­­­>mRNA­­­Translation­­­> protein   ○ Transcription   ■ DNA­­>RNA  ● 5’­­­>3’  ● Thymine become uracil   ● Sense strand or coding strand   ○ What the RNA polymerase will bind to   ● Transcriptional start site   ○ Synthesizing small segments of the chromosome ( known  as genes)    ○ The gene unit will start +1  ■   ○ Promoter is ­35TTGACA  and the ­10 TATA this is  recognized by a sigma factor binded to the RNA  polymerase   ● Sigma factors can vary under enviromental  conditions   ■ Note that if it is (­) it is consider upstream from the  +1   ○ Transcription bubble   ■ Where DNA unwinds   ○ Terminator   ■ Where transcription ends   ■ Stem and loop (that is G­C rich) formation causes  RNA polymer to pause and fall off  ■ Four or more uracil indicate that the polymer to fall  off   ■ Sometimes a protein known as RHO factor protein   ● Known as a  RHO dependent termination   ● Found in eukaryotes   ○ Denaturation   ■  When two strands of the DNA no longer touch   ■ G­C bonds are harder to break due to its hydrogen  bonding   ○ In prokaryotes transcription is equal ttranslation  ■ Ribosomes bind and makes mRNA into a proteins   ○ Translation   ■ Initiation   ● Has a start codon with a formal group (fmet)   ○ In the p side of the ribosome   ○ Amino acids come in on the A side and translates to the p  side  ● Energy source GTP   ● Initiation factors   ■ Elongation factors   ● peptidyl transferase   ● Peptide bond transformation   ■ Termination   ● Stop codon   ○ Replication  ■  DNA­­­>DNA   ● When making another DNA strand use DNA polymerase going  from the 5’ to 3’ direction with ​emplate strand   ○ Where the double helix is open is known as the  replication fork   ○ There is always agging and leading strand   ■ The​eading strand s constantly moving in one  piece   ■ The​agging strand (discontinuous strandis  moving in pieces known ​kazaki fragments   ■ In the end there is 2 copies for every strand of DNA  made  ■ You need a free 3’ OH group to attach  a  phosphate group to form the pyrophosphate group   ○ Replication ​emiconservative   ■ One strand is new the other strand already existed   ○ Replication occu​i­directiona around the  chromosome   ■ There is two replication forks around the loop of the  chromosome   ○ Takes 10min for E.coli to duplicate but 40 min for DNA  replication. This is speed up with multiple replication forks   ○ Hybridization   ■ When a new DNA is bonded   ● When making another RNA strand use RNA polymerase   ○ RNA   ■ Single stranded   ■ Contains AUGC   ■ There isNO​ thymine   ■ Has two OH groups one on the 3’ and one on the 2’   ● There iNO  presence of this second OH group at the 2’ carbon  on DNA   ■ Tree types  ● mRNA  ○ Messenger RNA  ○ Anti codons   ■ The counterpart of the amino acid sequence   ● rRNA  ○ Ribosomal RNA  ○   ● tRNA  ○ In a crucifix formation   ○ 20 amino acids =20 tRNA  ○ Sequence for proteins via the use of amino acids   ■ Prokaryotes have 16S RNA  ■ Eukaryotes have 18S RNA  ■   ○ Genotype  ■ Genetic makeup  ○ Phenotype   ■ Protein make up   ○ Nucleotide   ■ Phosphate + sugar base   ○ Nucleoside   ■ Sugar+ base  ○ Purine   ■ Adenine   ■ Guanine   ○ Pyrimidines   ■ Thymine  ■ Cytosine   ■ Uracil  ○ ​Codons  ■ Made up of three bases   ● Stop codons   ○ UAA   ○ UAG   ○ UGA   ■ These won't code for any amino acids  ● Start codon   ○ AUG.....methionine  ● Degenerate codons   ○ Has multiple codes for one amino acid  ○ DNA   ■ Antiparallel    ● 5’ and 3’ ends are always opposite   ■ Complementary base pairing   ● A​ples on​ees  ● Gas​inc​rs   ■ Double helix 


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