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1.6 & 1.7 Notes

by: Gail Chernomorets

1.6 & 1.7 Notes BIOL 251

Gail Chernomorets

GPA 3.2

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Week 4 notes 09/20 & 09/22
Medical Microbiology
Kurt Regner
Class Notes
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This 12 page Class Notes was uploaded by Gail Chernomorets on Friday September 23, 2016. The Class Notes belongs to BIOL 251 at University of Nevada - Las Vegas taught by Kurt Regner in Fall 2016. Since its upload, it has received 71 views.


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Date Created: 09/23/16
09/20 & 09/22 1.6 Prokaryotes Part II 2 Type of Prokaryote • 1976 • A new type of prokaryote was discovered • Methanogen - produce methane (CH ) 4 → flammable - anaerobes → anaerobic environment - wetlands produce marsh gas - digestive tracts of ruminants → cells were to difficult to get → Ex. cows, sheep, antelope - fart and burp methane constantly • Sequence of ribosomal RNA (rRNA) demonstrated that methanogens were not bacteria - hard to isolate • Archaea: new type of prokaryote - scientists isolated rRNA - physiologically, structurally, and biochemically unique - how the 3 domain tree of life started → proposes that at one tie a population of organisms were ancestors to Archaea and Eukarya Archaea • Prokaryotes • Superficially similar in appearance to the Bacteria, but many important differences • Archaeabacteria and Eubacteria are invalid terms ** Archaea are more closely related to Eukarya than the Bacteria are related to Eukarya Extremophiles • Archaea’s nickname • Examples - deep sea hydrothermal vent; underwater geyser, <100°C - Fly Ranch Geyser; hot springs 50-90°C - >90°C; near boiling sulfuric acid cave - salt pongs; ocean water evaporated; (10x saltier than the sea) - Gut methanogens; found in intestines of termites; make methane • Placing the Archaea into extremophile groups was an overly simplistic method of classification and ignored evolutionary relationships • Archaea isolated from human colon, in the oral cavity, on skin, soil, ocean and marshlands - microbiologists got better at finding Archaea - mesophilic environment - mesophiles - not necessarily extremophiles - No Archaea are known to cause disease in humans or animals, plants ** Nanoarchaeum equitans On exam • Obligate symbiont • One of the smallest organism • Marine hydrothermal vents and at Yellowstone hot springs • Obligate symbiont of a larger archaeon, Ignicoccus • 10 N. equitans have been observed on the surface of a Ignococcus cell • Nanobacterium does not have genes required for the biosynthesis of amino acids, nucleotides, co-factors, and lipids • Possible connection with endosymbiosis **Do Archaea perform photosynthesis? • No Archaea perform photosynthesis - not true photosynthesis • Halophiles used bacteriorhodopsin to absorb light and produce ATP - many pigments absorb different light - Light activated H pump - H enters cell through a ATP synthase - Not considered photosynthesis • Why is it not photosynthesis? - no electron transport chain - no CO 2fixation Summary • Structure - membranes - cell wall • Biochemistry - Methionine is the 1 amino acid rather than N-formylmethionine - RNA polymerase • Genetics - gene promoters - introns • Physiology - many live at temperatures and pH lethal to eukaryotes and bacteria Archaean Membranes • Unique membrane lipids • Very different from the Bacteria and Eukaryotes • **Ether linkage - Bacteria and Eukaryotes have an ester linkage • Stabilize membranes in the extreme environment Chemical Structure • Ring structures in fatty acids • Very long (40 C) side chains - common in the hyperthermophilic Archaea • Bacteria do not have ring structures in membrane fatty acids • Eukaryotes have sterols • Bacteria - straight hydrocarbon strands Lipid Monolayers • Some Archaea have a lipid monolayer • Other archaeal hydrocarbons fit the same template as those of bacteria and eukaryotes Archaean Cell Walls • All lack peptidoglycan • Some species have pseudopeptidoglycan - carbohydrate - similar to, but distinctly different from the peptidoglycan of Bacteria • Some species have cell walls with protein surface covers - S-layer - different First Amino Acid • In Archaeal polypeptide chain is methionine • Bacteria use N-formylmethionine **Archaeal RNA polymerase is similar to eukaryotic RNA polymerase - Archaea and Eukaryotes have a similar number of subunits and composition - More similar than bacteria in composition Archaeal promoters • Resemble eukaryotic promoters • RNA polymerase binds here (RNAP) • AT rich sequence resembles an Eukaryotic TATA box • Found at the start of a gene • RNAP is an enzyme of transcription Archaeal genes • Have introns - non-coding regions within genes • 23S, 16S rRNA, and tRNA genes • Bacterial genes do not have introns • Finished, uninterrupted gene • Prokaryotes & Eukaryotes have interrupted genes (don’t code for final product) • Eukaryotic genes have one or more introns Kingdoms within the Domain Archaea • The Domain Archaea is under revision due to an increase in rRNA sequence data • Archaea is influx Suggestion of Two-Domain Tree • Some archaea have eukaryote-like genes - actin-like protein - cell signaling → signal transduction - membrane bending proteins → endocytosis and exocytosis requires → membrane to bend • Currently a hypothesis 1.7 Viruses & Prions Viruses • Smaller than bacteria • Nanometer (10 ) – micron range (10 ) -6 - reproduce themselves • Obligate intracellular molecular parasites - made up of RNA and protein - have to have cell to replicate • Infectious • DNA or RNA • Acellular • Lack metabolic pathways - don’t have glycolysis (citric acid cycle) • Lack ribosomes • Evolve - Ex. Influenza A • Acquire new alleles/genes • Exceptionally diverse • Largest virus size is the size of the smallest bacteria Polythetic • A group that cannot be defined on the basis of any single shared character, but on overlapping combinations of characters shared by some of its members; define them by what they’re not - Type of genome - DNA, RNA, double- or single-stranded, positive or negative ssRNA, ssRNA requiring DNA intermediate, dsDNA requiring an RNA intermediate - Shape - Capsid structure - Presence or absence of an envelope - Presence of additional structures - Organisms they parasitize Virus sizes ** Do not need to memorize examples of virueses ** Need to know • Megavirus - 440 nm - discovered first of the 3 types • Mimivirus - 750 nm • Pandoravirus - 1000 nm - largest virus to date - Ex. Acanthamoeba polyphaga → Cause atypical type of pneumonia → Amoeba in aquatic environment • Largest viruses are in the same size range as the smallest bacteria • Largest viruses have same amount of DNA as parasitic eukaryotes Where do viruses fit? • Some proposed a 4 domain - viruses do not have a single evolutionary origin and there’s no valid location to add a 4 domain • No evidence backing the virocentric origin of life • Viruses are vehicles of horizontal gene transfer • From cells à viruses & from viruses à cells • Human chromosomes are full of nonfunctional viral genes • Believed viruses arose at 3 independent events • As long as there has been cells there have been viruses The Two Empires • Virus empire • Cellular empire • Viruses do not fit into the traditional Three Domain Tree • Never caught on and not a legitimate system ** Not popular Viral Mutation Rate • Viral mutation rate ~1 in - 10,000 nucleotides • Human rate is ~1 in billion nucleotides - a lot lower than viral rate • Low fidelity polymerases • Lack proof-reading enzymes • Reassortment is frequent - exchange nucleic acid segments with a different strains of the same virus - helps viruses evade host immune system and respond to selective pressure Where are viruses found? • Wherever we find cells Mycoviruses • Fungi - found in mushrooms Bacteriophages • attach to healthy basidiocaps Virion • An individual complete virus particle • Several terms are used to describe the virion shape - Helical - Polyhedral → Many sided → Icosahedral • Binal - pleomorphic - irregular shaped Ex. Pandora virus • Defining characteristic - diversity Capsid • Protein shell enclosing the nucleic acid - made up by many subunits → can be same or different - DNA or RNA - Viral enzymes • Built of large number of proteins called capsomeres • Capsid can be composed of 100s of same or different capsomeres Nucleocapsid • Nucleic acid and capsid Envelopes • Many animal viruses are surrounded by a lipid bilayer • Derived from host cell • Contain viral glycoproteins (sugar) required for infecting cells - bind to cell and trick to allow entry by receptors - lipid bilayer from host cell • Naked viruses - without envelopes A Brief History of Virology (Parallels microbiology) Dimitri Ivanowsky • 1892 • Botanist • Hired to find cause for disease • Tested filtrate (liquid) that passed through filter • Took yellow/brown infected leaves, grounded them up to catch the bacteria, and grew them with a ceramic filter • **Tobacco Mosaic Disease - causal agent could pass through ceramic filter because it was smaller • Plants get diseases like animals Martinus Beijerinck • 1898 • Famous microbiologist • Assumption was the cause of bacteria • The same experiment was performed as Ivanowsky but difference was that he took filtrate and boiled it; denatured proteins and nucleic acids • Said that viruses were a contagious living fluid Assumption during this time • Viruses were very small bacteria that no one could figure out how to grow • Not clear answer Foot & Mouth Disease • 1898 • Transmissible filterable virus • Foot and mouth disease virus (FMDV) - still around, highly infectious * used Coch’s postulates • Took infected tongue and used infiltrate and saw that filtrate was cause of disease Other Diseases • Yellow fever - 1902 - mosquito vector - can’t isolate bacteria caused by viruses • Bacteriophages - 1915 - viruses that infect bacteria • Rous Sarcoma Virus - 1911 - Oncogenesis → cancer in chickens - rous sarcoma virus → tumors in chickens • Virus cultivation in fertilized chicken eggs - 1931 - thought was viruses need living cell to be able to reproduce - to be able to cultivate viruses * Fall into category of virus when bacterial background was found to be negative. Crystallization • 1935 • Conclusive proof that viruses were not cells • Composed of protein and nucleic acid - DNA - RNA • Require a host cell for replication • Extraction from tobacco mosaic disease • 1 crystallization deactivated virus Franklin Roosevelt • 32 president • From ’33-‘45 • Afflicted at 39 • Polio Polio • Basic research on polio lead to an understanding of viral • Transmission - fecal/oral route • Host infection - through digestive system - attack neurons • Cytopathic effects - infected cell turns into virus making machine - disturbs homeostasis of organism • In vivo cultivation - fertilized chicken eggs • Immunology - aided by antibodies • Nucleic acid replication - RNA virus - Stimulated research • Vaccination - preventative treatment How do viruses make us sick? • Host cells are manipulated to producing viruses and not their usual function - changes in size and shape - cytoplasmic inclusion bodies →viral proteins →cant function normally - nuclear inclusion bodies - cells fuse and form multinucleated giant cells →giant cell with many nuclei - cell lysis → so full of virus cell → cells die - alter DNA/mutations → in host cell - transform cells into cancerous cells How do viruses infect? • Mucous membranes - degrades and enters • Respiratory tract - inhaled • Arthropod vectors - mosquitoes - tits/flees - lice • GI tract - contaminated food and water - digested • Trauma • Animal bite • Contaminated needles • Plant viruses - insects - mites - ticks - arthropod vector • Mechanical injury - ex. farmer tools nick an infected plant and transport to other plants causing all to be infected • Seed borne • Genitourinary tract - sexually Viral Host Specificity • Virion must bind to proteins found in the host cell’s membrane - receptor for normal cellular function • Lock & Key • Rabies virus infects neurons • Hepatitis B infects liver cells • Nonenveloped viruses attach via arrangement or shape of capsids - cant infect because no similarity in shape to receptors Virus Making Machine Steps 1. Attachment • Infectious virion attaches to healthy cell by cell membrane 2. Penetration • Enveloped enter via endocytosis or fusion • Nonenveloped enter via endocytosis 3. Uncoating • Host cell removes capsid • Endocytic vesicles low pH • Host cell proteases • Processing between - virus is uncoated by host cell 4. Eclipse phase • Interval between penetration and production of virions • Range in hours/days or even years if retro virus • Time it takes 5. Synthesis • Host cells copy nucleic acid and make viral proteins • Viral DNA escorted to nucleus by cell proteins • Replicated • Viral enzymes may be involved • Transcription by host 6. Assembly 7. Release • Lysis versus budding • At edge of membrane and cause it to become a membrane surrounded by infected proteins Prions • Neural protein • Not viruses • Infectious proteins • Transmissible spongiform encephalopathy - holes in the brain • Rare progressive neurogenerative disorders that affect both humans and animals • Spongiform changes associated with neuronal loss • Mad Cow disease BSE • Scrapies – sheep • Kuru - in New Guinea, eating brains of those killed as sign of respect - human version of mad cow disease/scrapies • Creutzfedt-Jakob (CJD) • Fatal Familial Insomnia - transmitted person to person - digestable • CJD and Fatal Familial Insomnia are inherited disorders • CJD, Kuru, and Fatal Familial Insomnia are human diseases • Consumption of diseased animals • Contaminated blood and blood products • PrP - nScmal cellular form • PrP - Scrapie - Sheep TSE - Incorrect shape - Incorrectly folded brain proteins PrP & PrP Sc • PrP cause abnormal folding of normal brain PrP C • Function(s) of the normal prion proteins is not completely understood • The abnormal folding leads to brain damage and the characteristic signs and symptoms of the disease British Cattle • Cattle were routinely fed meat and bone meal as a protein supplement for decades • Meat and bone meal are processed remains from slaughter houses • Parts of cattle that humans don’t eat go to dog food and cattle feed • Sometime during the early 1980’s shape and/or cattle with TSE were included in the meat and bone meal processes - infected bone meal added to cattle feed • Starting in the mid-1990’s more than 100 individuals developed Creutzfeldt- Jakob Disease (vCJD) from consuming tainted meat - caught attention because normally, vCJD was an inherited disease - typically, 3 cases or less per year were reported for the entire UK - 4.3 million cattle were destroyed in 1998 • Connection with mad cow and scrapies could lead to vCJD • Exceptionally resilient US & Canadian Cattle • A small number of US and Canadian cattle have been diagnosed with Mad Cow Disease (BSE) • No blood test available to know if infected - signs and symptoms are seen and only way to know if infected is to slaughter and examine the brain Blood Donations • No test for vCJD to screen blood donors - (v=variant; human version of Mad Cow Disease) • Ineligible to donate blood if: - resided in the UK for 3 months or longer from 1980-1996 - received a blood transfusion in the UK or France from 1980 to present Standard Cooking Recommendations Sc • **DO NOT DESTROY PrP IN MEAT • Amount needed would essentially be entirely burnt meat • Contrary to popular belief PrP can be destroyed by: - Autoclaving → But has to be longer and higher pressure - Sodium hypochlorite and sodium hydroxide → to surface - Proteases → Break up - Animal rendering → Butchered goes to dog food and leather → Parts of cow we don’t eat used to eliminate prions - Incineration → Will destroy PrP are not indestructible, but specific protocols must be strictly followed


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