Lecture 11.1. Virus- Not life because it cannot replicates itself. Instead, they are using host cell.2. Virus structure- Protein coat (Capsid): core that contains strands of nucleotides.- Circular DNA, Linear RNA, not like a living cells.- Single or double stranded- Virions, virus particle: lacks cytosols and plasma cell membranes.a. Helical shape: loop shaped virusb. Icosahedral shapes- 20 equal triangular- Basic structure for dorm- Maximize internal capacity of structure in a very small space: mold more in less space.c. Binal- Complexes viruses are binal (complex or irregular) shaped.- Have both helical and icosahedral- Do not affect how virus can be, highly variable: viruses are very small.d. Bacteriophage: viruses that infect bacteria.e. The basic of viral replication -> Parasitic- Virus enters the host cell Virus insert its nucleotides (DNA Master) and the host cell becomes virus making machine. New viruses are born; cellular explosion.- DNA master: the nucleotides inside virus. This DNA inside is programmed to trick the host cell making new protein. 3. Prions- cause Transmisable spongiform Encephalopathies (TSEs): Diseases that are involved sweet fatal brain diseases.- Slow viruses: existing time gap between infected time and detected time.- Replication: like virus, abnormal prions infect normal prions, and the infected once-normal prions infect other normal prions.- Prion contains no genetic material (no RNA or DNA): Abnormal prion protein forces to misfold in the normal protein=> bogue protein- Disease is passed exclusively through proteins.- Inherited through proteins- Prions are very effective selection agent.4. Three domain modelA. Key traits common to bacteria and archaea.- Unicellular; no mitosis- Binary fission replication: Asexual- Un-enclosed DNA, single ring shaped chromosome.- No organelles.- Photosynthetic mechanism- Do exchange some genetic information with each other through horizontal gene transfer (lateral transfer) but they do not any predictable gene exchange through like sexual reproduction.B. Eukaryotes- Multicellular- Compartmentalized: organelles- Sexual- Mostly largeC. Protists- Misleading.- This term was used as catch all for small organisms that didn’t really categorized in Eukaryote kingdoms.- Paraphyletic group.Lecture 12.*”Prokaryotes”: cause they are paraphyletic.1. Differentiate the “prokaryotes” from the eukaryotesProkaryotes EukaryotesUnicellularity No multicellular: univellularMulti or uniInternal structure No membrane bounded HighlyorganellesNo cytoskeletonNo enzymecompartmentalized, many organellesChromosomes Single, circular DNA chromosome.Membrane-bounded nucleus with multiple linear chromosome.Cell division Binary fission MitosisGene Transfer Lateral transfer RecombinationCell wall Ubiquitous (peptidoglycan; bacteria, polymer of sugars and amino amids that forms in interior cell wall or psuedomurein; archean, similar polymer to peptidoglycan) In some organisms (nopeptidoglycan)If Gram stain-> pink/redBacteria:Gm (+): multiple peptidoglycan layers -> purple stained. Gm (-): one thin peptidoglycan layer -> red/ pink stained. Archaeans are all Gm (-) since they don’t have peptidoglycan layer.Flagella -Simple, single fiber-rigid-they spin in order to moveVery complex, 9+2 structureSize -Typically small-very misleading -> initially notice one. Typically large.*Horizontal transfer: do not give a trait via reproduction- Web of life- ex) Thermotoga maritime: survive in extremely high pemperature. Insignificant traits are not passed vertically but can move one branch to another. (One species to another.)2. Bacteria classificationA. Shape (rod: bacillus, sphere: coccus, spiral: spirillum) B. Metabolisma. Respiration- Aerobes: need oxygen to live- Anaerobe: poisoned by oxygen- Facultative anaerobes: it can live both anaerobe and aerobe environment. They prefer to be at the top since aerobic respiration generates more ATP.- Aerotolerant anaerobes: do not require oxygen as they metabolize energy anaerobically. Unlike obligate anaerobes however, they are not poisoned be oxygen. They can be found evenly spread throughout the test tube. b. Food(1) Autotrophs (self feeders): light+water -> break down CO2 to make sugar.- Photoautotrophs: catch light and produce oxygen as by product. Need chlorophyll- Chemoautotrophs: gain energy by breaking the chemical bonds of inorganic chemicals to make organic material; sugars. They use this energy instead of the energy from sun light to break down carbon dioxide in order to get carbon. (no need sunlight)(2) Heterotrophs (other feeders): including decomposers and pathogens.- Photoheterotroph: use bacterio-chlorophyll and hydrogen sulfide. Cannot break down carbon dioxide, so carbon source is from other organism. Energy comes from sun butcarbon comes from eating other organism. C. Gram + or –D. Motile or notE. Photosynthetic or notF. Unicellular, colony forming, or filamentous- Some prokaryotes are colonial and some are filamentous, while some exist simply as individual cells.3. BacteriaA. Gram (+) bacteriaa. Low GC Gram (+) can be dormant for long periods (endospores)- In harsh environment, most of the member can produce endospores that can survive in harsh (high temperature) environment.- Some endospores may not activate for millions of year and come back from dormancy. When it is active, it divides to form multiple new parent cell.- Toxicb. High GC Gram (+) Bacteria are filamentous.- Look like fungi.- Reproduce: break out from original cell.- Source of anti-bacterial; bacteria kill other bacteria- Ex) Actinomyces sp: break down organic soil; smell after rain.B. Gram (-) bacteriaa. Hyperthermophilic bacteria (ex. Thermotoga Maritima) and hadobacterica (ex. Deinococcus Radiodurans) are extreme heat lovers.- There is not a lot phenotypically difference between them.b. Cyanobacteria are critical photoautotrophs.- Not single species, very diverse group- Same internal membrane system- Chloroplasts are derived from cyanobacteria; photosynthesis- Gram (-)- Bloom of cyanobacteria. (giant colony)c. Spirochetes have axial filaments and are common pathogens.- Gram (-)- Heterotrophs- Mobility: axial filaments rotate inside spiral kit.- Borrelia burgdorferi causes lyme disease.- Syphilis.d. Chlamydias are the smallest, obligate parasitic cocci.- Gram (-)- Cause STD- Difficult iron infectione. Proteobacteria have very diverse metabolic pathways.- hargest, most diverse.- Purple bacteria- Photoheterotrophs,
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