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238 Cards in this Set
- Front
- Back
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what are the requirements for an organism to be considered alive? |
composed of cells, able to metabolize, growth, reproduction, evolution, response to external stimuli, and homeostasis |
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what are microorganisms? |
bacteria, fungi, algae, protozoa, and archaeons |
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what term refers to an organisms evolutionary history? |
their phylogeny |
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which domain(s) possess a nuclear membrane? |
only eukarya |
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which domain(s) possess membrane bound organelles? |
in rare cases bacteria and archaea, always in eukarya |
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which domain(s) possess a plasma membrane? |
they all do, the eukaryotic and bacterial membranes resemble each other while the archaeic is different |
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which domain(s) possess a cell wall. |
Nearly all bacteria and archaea, and some species of eukarya |
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which domain(s) possess RNA polymerase |
they all do... bacteria has a single polymerase, archaea have a single polymerase similar to eukaryotic Pol 2 and eukarya has 3 main polymerases |
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which domain(s) possess histones? |
Archaea and eukarya do, and bacteria possess histone like proteins |
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What advantages to microbes have in research? |
they grow rapidly, cheap nutrient sources, facilitate production of enzymes, have a small number of genes, and are easy to genetically manipulate |
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What theories exist about the first microbial life? |
1) "prebiotic soup" Miller Urey 2) Iron containing surfaces Günter Wächtershäur |
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what are macro molecules? |
polypeptides, mRNA, DNA, proteins.. NOT amino acids they are too small and singular |
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Describe the atmosphere of early earth |
small amount of oxygen, lots of carbon dioxide and nitrogen gas, it was a reducing atmosphere, hydrogen gas was present, |
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Discovery of ribosomes indicated that life on early earth was based on: ? |
RNA |
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What is the first living organism? |
Progenote: cell stores information in genes not yet linked together on chromosomes |
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Do bacteria undergo sexual reproduction? |
no, they undergo lateral gene transfer |
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How do bacteria contribute to the nitrogen cycle? |
convert nitrogen present in organic carbon back to N2 gas through denitrification/ amonia oxidation |
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know this |
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What was the first vaccine produced? |
cowpox used to vaccinate for smallpox, Edward Jenner 1796 |
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Who used microscope to see microorganisms for the first time? |
Anton Leeuwenhoek, 1600's |
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Who disproved the theory of spontaneous generation using a swan necked flask? |
Louis Pasteur, 1860's |
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Who practiced infection control (washing hands, etc)? |
Joseph Lister, 1860's |
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Who identified Bacillus anthracite as the cause of anthrax? |
Robert Koch, 1876 |
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Who discovered penicillin? |
Alexander Flemming, 1926 |
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Who developed the polio virus vaccine? |
Jonah Salk and Albert Sabin, 1950's |
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Who proposed the endosymbiotic theory? |
Lynn Margulis, 1966 |
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Who invented PCR? |
Kary Mullis, 1983 |
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Who porposed the 3 domains of life? |
Carl Woese, 1990 |
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Who published the first bacterial genome? |
Craig Venter, 1995 |
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What shape is a coccus bacteria? |
spherical |
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What shape is a bacillus bacteria? |
rod |
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What shape is a vibrio bacteria? |
curved rod, "comma" |
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What shape is a spirillum bacteria? |
spiral |
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What shape is a pleiomorphic bacteria? |
unidentified; irregular |
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What are hyphae? Mycelia? |
branching filaments of bacteria are called hyphae, tufts of hyphae are called mycelia |
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what are trichomes? |
smooth, unbranched chains of bacteria, e.g. cyanobacteria |
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Describe Staphylococcus aureus |
a Gram-positive coccal bacterium that is frequently found in the human respiratory tract and on the skin. It ispositive for catalase and nitrate reduction |
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what size are bacterial cells typically? |
Usually smaller than eukaryal cells (bacteria are often 0.5‒5 μm in length) |
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what is in the cytoplasm of baceterial cells? |
hosts the nucleiod regions, plasmid, inclusion bodies |
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What are some examples of inclusion bodies found in bacterial cells |
• Poly-hydroxybutyrate granules: carbon storage – (PHB) • Polyphosphate: phosphorus storage • Sulfur globules: sulfur storage • Gas vesicles: buoyancy control • Carboxysomes: location of carbon fixation reactions • Magnetosomes: organelle associated with direction finding |
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what is rubisco? |
Part of the krebs cycle… most abundant protein/enzyme on earth. Responsible for the fixation on CO2.
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describe the roll of FtsZ in cell wall synthesis |
protein forms the z-ring which is attached to the inner plasma membrane, and when it contracts it beings the cell envelope inward |
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describe the roll of MreB in cell wall synthesis |
polymerizes into filaments, forming long helical bands inside plasma membrane. Provides structure |
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describe the roll of ParM in cell wall synthesis |
responsible for moving copies of the plasmids to opposite sides of the cell.. parM gene is located on the plasmid |
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What are hapanoids? (bacteria) |
cholesterol like molecules found in the plasma membrane |
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What are the key functions of proteins found in the plasma membrane? |
1) controlling access of materials to cytoplasm 2)capturing/storing energy (ETC, photosynthesis) 3)environmental sensing and signal transduction |
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What are examples of active transport? |
co-transport (symport and antiport) and ABC transporters (ATP Binding Cassette) |
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describe the process of protein secretion in bacteria |
Sec B proteins bind to signal peptide as it leaves the ribosome, delivers it to SecA, which then associates with SecYEG (a membrane channel complex). ATP hydrolyzed and the movement of protein out of cell is facilitated |
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describe the structure of the bacterial cell wall |
matrix of crosslinked peptidoglycan molecules |
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Describe the structure of peptidoglycan |
glycan backbone of alternating N-Acetylglucosamine and N-Acetylmuramic acid. NAM carries chain of amino acids that crosslink |
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describe how peptidoglycan is made? |
1) NAM synthesized and linked to UDP 2) NAM linked to bactoprenol 3) NAG added to NAM 4) Bacterol flips to periplasm, disaccharides crosslinked to chain 5) Bacterol flips back |
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How are amino acids in peptidoglycan crossinks different than normal amino acids |
Several of the amino acids found associated with NAM inpeptidoglycan are unusual D sterioisomers |
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What effect does Bacitracin have on bacteria? |
interferes with the dephosphorylation of C55-isoprenyl pyrophosphate, a molecule that carries the building-blocks of the peptidoglycan bacterial cell wall outside of the inner membrane -- used as an antibiotic |
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differentiate between lysosome and lysostaphin |
lysosome will cut the D amino acid crosslinks in nearly all bacteria where lysostaphin will only cut specific staphyococcus species |
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describe how penicillin works (B lactam family) |
has a similar structure to peptoglycan and tricks crosslinking enzymes to bind to the antibiotic and form a bond -- stops the bacteria from growing |
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What are B-lactamases? |
antibiotic resistant enzymes, hydrolyze the C-N bond in the B-Lactam ring so it cant bind |
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Describe the process of the gram stain |
bacteria stained with crystal violet, iodine stabalizes the violet, alcohol removes the stain of gram neg cells, saffarin stains the neg cells pink (the pos cells are still purple) |
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what role does alcohol play in the gram stain process? |
The alcohol decolorization step shrinks the large poresin the Gram-positive cell, helping to lock the crystalviolet stain in. The alcohol also may strip away some of the outermembrane lipids in the Gram-negative cells, makingthem more likely to lose the initial crystal violet stain. |
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Describe the morphology of a gram positive baceria |
thick cell wall, exposed to the environment, also contains teichoic acid and lipoteichoic acid which is intermingled with the the peptidoglycan |
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describe the morpholofy and gram negative bacteria |
think peptidoglycan layer supplemented with an outer membrane. Outer membrane is non-traditional with outer leaf containing lipopolysaccharides (Lipid A, core polysaccharide, and the O side chain) |
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how does nutrient transport vary in gram positive to gram negative bacteria? |
In gram positive there are pores that nutrients can travel through whereas in gram negative a TonB receptor (complexed with ExbB and ExbD) is required to allow nutrient transport into the periplasm. Dependent on bacteriophage H8 |
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how do molecules get out of a gram negative bacteria? |
Some move from theperiplasm to outside directly(these are known asautotransporters and arerare). Some use single-step (neverentering the periplasm)transport systems. E.g. TypeIII secretion systems |
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describe the flagella of a bacterial cell |
provides motility. Spiral, hollow, rigid fillaments. Can be polar or peritichous. Composed of 3 pieces: 1) the filament 2)Hook protein (connected to basal body) 3)basal body (disc that produces torque) |
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describe the motility from flagella |
Energy to spin flagella derived from proton motive force (PMF). Spinning one way produces a “run” (directional movement)while spinning the other way (clockwise) produces a “tumble”(non-directional movement) |
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what are some types of non-flagellar motility? |
Gliding motility: smooth sliding over a surface, not well understood (myxobacteria, cyanobacteria) Twitching motility: slow, jerky process using fibers(pili) that can be extended, attached to a surface, andpulled back to pull along a surface (N. meningitidis, P.aeruginosa) Polymerization of actin-- further explained later |
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describe polymerization of actin |
allows for propulsion ofbacteria into adjacent cell.. actin pilli fibers allow the shigella to move into adjacent cell.. conjugated plasmids can be rapidly transferred from cells that carry it to cells that do not |
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differentiate between pilli (or fimbri) and the sex pilus |
sex pili refers to conjugation structures (sending DNA plasmid from one bacteria to another) whereas the pili or fimbri refers to adherance |
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what does a "holdfast" of polysaccharides refer to? |
extensions of the cell envelope that increase surface area for absorption and allow the bacteria to adhere to surfaces |
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what is the function and structure of a capsule? |
Thick layer of polysaccharides surrounding some cells... can provide adhesion, defense against host immunity,protection against drying out (desiccation.).. also form biofilms e.g. plaque) |
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what are surface arrays? |
crystiline layer of protein found in gram +/- costs a lot of resources to make but is worth it, acts as armor for the cell (prevents infection by bacteriophages, blocking penetration by predatory bacteria, shielding from immune system) |
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what features does bacterial classification depend on? |
• Size/shape • Gram type • Colony morphology • Presence of structures such as capsules/endospores • Physiologic/metabolic traits (see Ch. 13) • DNA sequence data (in more recent years) |
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what is the principle of priority? |
The principle of priority ensures that the first validly named, described nametakes precedence. |
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describe the morphology of a eukaryotic cell |
Membrane bound nucleous Usually larger thanbacterial/archaeal cells Usually contain intracellularcompartments (organelles) May possess a cell wallstructure Complex internalcytoskeleton in place |
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what does it mean for mitochondria and chloroplasts to be semi autonomous? |
Each has their own DNA, ribosomes, transcriptionmachinery, and can replicate independently of the rest ofthe cell. |
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describe the cell wall of eukarya |
Fungi: composed of chitin Algae: composed of cellulose, but diatoms have cell wall made of silicon Protazoa: no cell wall for the most part, sometimes for a brief period in the cyst stage |
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what linkages do cellulose and chitin in eukaryalcells |
B 1,4 linkages between sugars for strength and ridigity |
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describe the flagella of a eukaryotic cell |
flexible, covered by cell membrane, microtubule segments are transported out along the outside of the axoneme via an intraflagellar transport system |
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differentiate between motion cause by bacterial and eukaryotic flagella |
bacteria: motor in membrane turn flagella in a screw like motion -- energy from proton motive force eukarya: motion caused by Dynein spokes alide microtubues along eachother within the axoneme, bends the axoneme and whips flagella. Energy from ATP synthesis |
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What is an amichondriate? |
eukaryotic cell without mitochondria |
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What are giardia? |
oldest species of eukaryotes, also referred to as diplomonads.. no mitochondria |
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be familiar with the tree i guess |
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describe Saccharomyces cerevisiae |
Model Fungi: -compartmentalized into membrane bound components -controls shape via cytoskeleton -cell wall is chitin based -heterotrophic -inexpensive and easy to manipulate, called brewers yeast -used to study gene expression |
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describe giardia lamblia |
Model Protozoa: -can be heterotrophic or photosynthetic -most dont have cell walls -some are flagellate -reproduction is varied, some have 2 nuclei -OLD (no mitochondria) provides clues to the origin of eukaryotic life |
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describe Dictyostelium discoideum |
Model Slime Mold: -slime molds have 2 types: cellular (discoideum) and acellular (Physarum) -generally indivisual cells, sometimes will aggregate to form multicellular mass (cellular) or will fuse to form multi-nucleii aggregate (acellular) -used to study intracellular communication and evolution of multi cellularity |
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describe Chlamydomonas reinhardtii |
Model Algae: -single celled algae (some are multi) -varies in size shape and motility -autotrophic -cell wall made of cellulose -2 flagella good for studying eukaryal flagella biogenesis/function. -studied because of its ease of growth and durability -used to study details about cellular function of eukaryotic flagella |
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how does Yeast and Chlamydomona's ability to alternatehaploid/diploid stages benefit them? |
Allows for better survival and genetic variation |
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How does Saccharomyce's ability toundergo meiosis to forman ascus benefit it? |
Haploid mating types canfuse to reproduce sexuallyor be maintained by asexualmitosis -- makes an armour spore type thing to withstand harsh conditions |
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What evidence supports endosymbiotic theory? |
-Mitochondria/chloroplasts resemble bacteria in both sizeand shape. -Arrangement of double membranes around these structuresis consistent with ingestion idea. -Each has its own DNA, and that DNA sequence is much morelike bacteria than eukaryotic DNA. |
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how does Metronidazole (antibiotic used particularly foranaerobic bacteria and protozoa) work? |
absorbed by anaerobic bacteria and protozoa reacts with reduced ferredoxin, which is generated by pyruvate oxido-reductase – anenzyme found in anaerobe... reduced nitroimidazole intermediates form linkages with cysteine-bearing enzymes,thereby deactivating these critical enzymes |
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why might the phytoph be more related to algae? |
because cellulose in the cell walls |
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what are some beneficial roles of eukaryotic microbes? |
- produce lots of oxygen -many are able to degrade cellulose and recycle plant matter better than animals |
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what are lichens? |
microbes symbionts... fungal spegies that has a symbiotic relationship with 1-2 photosynthetic species. Not intracellular. |
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what are some distinctive properties of archaea? |
– Size is usually 0.5–5 μm in diameter. – Both Archaea & Bacteria usually possess singular,circular chromosomes & lack a membrane-boundnucleus. – Archaeal DNA is complexed with histones (likeEukaryotes). – Many of the DNA replication enzymes of Archaea“look” like those of Eukaryotes. – The Archaea plasma membrane structure is unique tothis domain. |
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how is histone wrapping different in archaea and eukarya? |
octamer of histone proteins in eukarya, tetramer in archaea |
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Example of homologue between archaea and eukarya |
Ta0583 is an actin homolog in Thermoplasma acidophilum that resembles eukaryal actin. |
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Example of homologue between archaea and bacteria |
Cytoskeletal proteins from Methanothermobacterthermoautotrophicum and Methanopyrus kandlerimore closely resemble bacterial cytoskeletal proteins. |
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How is the plasma membrane of archaea is different in composition to bacterial and eukaryalmembranes |
in bacteria/eukarya: fatty acid linked to glycerol 3 phosphate with ester links archaea: glycerol 1 phosphate with ether links.. carbon chains made from isoprenoid (phytanyl) |
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How do some archaea have a monolayer? |
n some archaea the phytanyl units are joined to give biphytanyl and so thephospholipid membrane is a monolayer rather than a bilayer |
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what is the cell wall composed of in archaea |
pseudomurein (different than peptidoglycan) |
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How does pseudomurein differ from peptidoglycan |
Instead of NAM there is NAT.. NAT attaches to L amino acids instead of D amino acids |
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what is the significance of the B1,3 linkages and the L amino acids in archaea? |
the B 1,3 links make the archaea insensitive to lysosomes (which attack 1,4) and the L amino acids make them insensitive to penicillin (which attacks D amino acids) |
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describe the archaea flagella |
Similar to bacteria in that they rotate to move the cell. Different from bacteria because they are thinner (10‒14 nm vs. 20‒24 nm). Usually composed of two or more different versions of flagellin proteinLikely growing from BASE rather than from TIP
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what are two major groups of archaea? |
crenarchaeota and euryarchaeota |
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Describe crenarchaeota. What are some examples? |
Many members are thermophiles or hyperthermophiles, mesophiles and Psychrophile. Also acidophilesand barophiles |
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what are some adaptations for survival that crenarchaeota possess? |
- Tetraether lipids/lipid monolayers - More α-helical regions in proteins - More salt bridges/side chaininteractions in proteins - More arginine/tyrosine, lesscysteine/serine - Strong chaperone proteincomplexes - Thermostable DNA-bindingproteins - Reverse DNA gyrase enzyme toincrease DNA supercoiling |
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What are some examples of Euryarchaeota? |
Methanogen and halophiles |
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Describe the morphology and function of methanogen |
They reduce CO2 with H2 to produce methane (CH4) and water (H2O).. energy released can be used to fix carbon. All identified methanogens are strict anaerobes. The methane produced in these areas forms gas from humans and combustible air from swamps |
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Describe the morphology and function of halophiles |
Require NaCl concentration greater than 1.5, produces energy through an odd form of phototrophy Doesn’t use chlorophyll or an electron transport chain, it uses bacteriorhodopsin to harness light energy and produce aproton motive force |
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how do halophiles deal with osmotic shock and loss of water? |
theymaintain a very high intracellular K+ concentration tooffset the very high extracellular Na+ concentration |
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what sort of micro filter would you use to remove all bacteria?
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1 micron or 0.2 micron filters |
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what is the general size of bacteria? |
Diameter between 10 and 100 nm |
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describe the viruses viral genome |
single or double stranded DNA/RNA. Mostly linear although there are a few circular and segmented. Nucleic acid and capsid are called nucleocapsids. |
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describe helical and icosahedral morphologies |
helical: capsomeres form a helix and the capsif resembles a hollow tube icosahedra: capsomeres form an isohedron with each capsomere making a face |
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what does HA and NA stand for? |
HA: Haemagglutinin - cause red blood cells to agglutinate NA: Neuraminidases are enzymes that cleave sialic acid in glycoproteins |
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differentiate between enveloped and non-enveloped viruses |
Enveloped viruses have a lipid bilayer around the capsid. Nonenveloped viruses do not have this feature, the virus is “naked.” |
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describe two ways influenza A can develop variation? how is it able to do this? |
1) There can be a drift where the proteins on the enveloppe change 2) there can be a fusion, for example a highly pathogenic avian strain mixing with a human strain and becoming a highly pathogenic human strain The fragmented nature of the influenza A genome allows the exchange of gene segmentswhen two or more influenza viruses infect the same cell |
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What are 5 steps of viral replication? |
1) recognition and attachment to the host 2) penetration of the host cell’smembrane, capsid disassembly 3) expression of viral genes tomake proteins (synthesis) 4) replication of viral genome 5) assembly of new virus particles and exit from the cell. |
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what is the most important part of viral replication? |
Entry into the host cell |
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What external features of the cell would be recognized as receptors? |
transporters and other intermembrane molecules |
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Why bother with specific receptors? |
you have to trick the cell into thinking the virus is something it wants, or look for conserved receptors that are common, or break down the cell wall/membrane |
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Do viruses need to take off your protective coat? |
yes |
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Rhinoviruses - common viral infective agentsin humans - predominant cause of thecommon cold. |
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HIV |
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Retrovirus -Retroviridae is afamily of SS-RNAenveloped virusesthat replicate in ahost cell through theprocess of reversetranscription. |
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describe a viruses entry into bacteria |
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do plant viruses have specific receptors to recognize on their host cell? |
no, only animal viruses do |
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have are bacteriophages cultivated? |
a liquid culture of bacteria is inoculated with phage.. with virulent or lytic bacteriophages the virus will eventually destroy the host cell. As bacteria are destroyed liquid becomes clear and you can filter the dead bits out
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describe temperate or lysogenetic bacteriophages |
they can exist in a non-lytic "prophage" phase where they are incorporated into the host (lysogen) DNA but the genes are suppresed. Under certain conditions they will be transcribed again and become lytic |
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how are mammalian cells cultured? |
incubated at 37 degrees, 5% C02. Cells divide until they cover the substrate, then trypsin is added to dislodge the cells from the surface of the medium. Dislodged cells plated at a lower density and continue growing |
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what are cytopathic effects? |
visible changes in cell morphology as a result of animal viral infection.. may involve the rounding or detachment of infected cells or the fusion of cells into a mass known as syncytium |
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how are plaques formed? |
viruses are mixed with agar and added to host cells (either plate of bacteria in nutrient agar or cells growing on dish - agar layer on top after). The viruses start to infect cells, confined to the plate. Each virus will start in one spot and move out until we can start to see spots |
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what are some methods of viral quantification? |
Usually measured as a titer,or concentration of a virus preparation Direct Count (EM); Plaque assays; cytopathic effects (CPE);Endpoint Assays- Lethal dose 50 (LD50) Viral RNA is treated with reverse transcriptase to turn it into DNA.. the DNA can then be amplified and quantified. |
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how are viruses purified with differential centrifuging? |
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how are viruses purified with gradient centrifuging? |
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how are chicken eggs used to make vaccine? |
egg has been fertilized 13-14 days previously, then you inject the virus and allow it to replicate. The higher number the more people you can inoculate with a given batch of virus. |
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What are HeLa cells? |
the first human line derived from a woman suffering from cervical carcinoma.. "immortal" line of cells that vary somewhat from typical human cells |
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how does a direct count work for viruses? |
a known quantity of microscopic markers are added to a sample of the purified virus. then placed into a grid and viewed with an electron microscope. Beads (markers) let to know the exact volume of liquid applied to the grid. |
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what is Bacteriophage lambda? |
Model lysogenetic virus: a phage that can integrate into the genome.. it has a foggy plaque that we call turbid. Having the virus in the genome makes them immune to infection of the same virus going into the lytic cycle |
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Describe the process of quantification through Haemagglutination assay |
Exploits trait of some viruses to stick to red blood cells (RBCs), causing them to from a gel mat. When there are enough virons binding to RBCs they clump together and a "sheild" well is noted. If there are not enough a "button" well will form - all of the RBCs sink to the bottom. |
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what are the prons and cons of Haemagglutination assays? |
Pros: Cheap, easy, fast; no microscope needed Cons: Some viruses won’t do this; doesn’t differentiateviable/non-viable viruses; doesn’t give a virus number |
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Describe the process of quantification through endpoint assays |
some viruses don't cause plaque formations or RBCs agglutination... instead the viruses are serial diluted and injected into host cells or animals. Lethal Dose 50: Amount of virus needed to kill 50% of the subjects is recorded. Tissue culture infectiousdose 50 (TCID50):Amount of virus neededto induce a CPE in 50%of cultured cells |
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Describe factors in choosing a viruses name |
-Simple letter/number combinations (T4 phage)
-Organism(s) they infect (tobacco mosaic virus) -Location of discovery (Ebola River, Zaire) -Appearance (coronavirus, “crown”) -Disease caused (hepatitis viruses) |
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Describe theICTV (International Commitee onTaxonomy of Viruses)classification scheme |
Classify viruses basedon Order, Family,Subfamily, Genus, andSpecies |
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Describe the Baltimore classification system |
Based around mRNA production methods, separates viruses into seven classes |
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What are Koch's postulates? |
1) the microorganism or other pathogen must be present in all cases of the disease 2) the pathogen can be isolated from the diseased host and grown in pure culture 3) the pathogen from the pure culture must cause the disease when inoculated into a healthy, susceptible laboratory animal 4) the pathogen must be reisolated from the new host and shown to be the same as the originally inoculated pathogen |
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What are viroid? |
Consistonly of nakedRNA
are extremely small (less than 400 nucleotides) Have a high degree of internal complementarity Are resistant to ribonucleases So fa, only observed to cause disease in plants |
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What are satellite viruses and satellite RNAs |
They need a helper virus for replication; They contain a protein coat. Satellite viruses’ genome encodes the protein coat. Satellite RNAs use a helper virus to encode the protein coat. |
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How does Reverse transcriptase PCR work? |
RNA is isolated. Primer, RT, nucleotides added RT makes a complementary DNA copy of the RNA. Sample is heated to denaturestrands and inactivate RT. Primers, Taq pol, andnucleotides are added. Taq pol makes a second DNAstrand. Further PCR cycles can amplifythe amount of DNA produced. |
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Which Domain contains the viruses? |
They are not classified at the domain level. |
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What is the most common way for enveloped viruses to enter animal cells? |
The virion fuses itself to the cell membrane. |
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Viruses that have icosahedral symmetry have ________ faces and 12 vertices resulting in a spherical appearance |
20 faces |
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Most viruses with helical capsid symmetry contain _______ as their nucleic acid. |
ssRNA |
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The eukaryal cell emerged on Earth approximately ______ years ago. |
2 billion |
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Chloroplasts most likely originated from which of these independent organisms? |
cyanobacteria |
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Which of these is correct regarding subunit rRNA? |
It serves the same biological function in all organisms and its sequence changes very slowly over time. |
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Many of the hyperthermophilic crenarchaeotes that have been grown in culture are also _____ . |
acidophiles |
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Which member of the Archaea domain is a parasite of the archaeon Ignicoccus hospitalis and has one of the smallest genomes of all living microbes? |
Nanoarchaeum equitans |
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what is the composition of microbes? proportionally by dry weight |
Polypeptides (50-55%) Nucleic Acids (DNA,RNA) (2-5%) Lipids (10%) Polysaccharides (6-7%) |
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What nutrients do macromolecules need? |
C source – Glucose or Lactose, or Sucrose etc. N source – NH4Cl or (NH4)2SO4, etc. P source -- NaH2PO4, Na2HPO4, etc. S source - MgSO4 etc. Various micronutrients: including several metal ions (Na+, Mg2+, Mn2+, Fe2+, Zn2, Co2+etc. |
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phototroph vs auxotroph |
Prototroph: synthesizes all cellular components from basic nutrients glucose, ammonia, phosphate and sulphate, will grow in a mineral salts medium with a carbon source Auxotroph requires supplements in order to grow e.g. a vitamine, amino acid(s), purine, pyrimidine. |
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source of electrons: organotropphs vs lithotrophs |
Organotrophs: electrons from organic molecules (e.g., glucose) Lithotrophs (‘rockEeaters’): electrons from inorganic sources (e.g., H2 gas , NH4, H2S, and elemental sulfur) |
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source of carbon: autotroph vs heterotroph |
autotrophs assimilate carbon from things like carbon dioxide whereas heterotrophs need carbohydrates, amino acids, etc. |
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energy source: chemotroph vs phototroph |
phototrophs make energy from light through photosynthesis, chemotrophs breaks down preexisting organic molecules |
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know this well |
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what are two ways to assimilate ammonia into amino acids? |
1) GS-GOGAT works best at low ammonium concentra&ons. 2) GDH (glutamate dehydrogenase) works best at high ammonium concentra&ons. |
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3 different mediums, glucose added at progresively higher concentrations |
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list different type of oxygen dependent and independent organism
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-Aerobes grow in the presence of oxygen. -Obligate aerobes REQUIRE oxygen. -Microaerophiles grow best when there is less oxygen than normal. -Anaerobic growth occurs without oxygen. • -Aerotolerant anaerobes aren’t harmed by oxygen but don’t use it, either. -Obligate anaerobes cannot grow when oxygen is present. -Facultative anaerobes CAN use oxygen but can also grow in the absence of oxygen. |
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Effects of oxygen on microbial growth |
Often determined by what defenses are available against oxygen’s negative effects in the cell.. molecular oxygen can made byproducts that are detrimental to other things in the cell, like proteins and lipids (hydroxyl radicle, hydrogen peroxide). |
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how do species deal with the toxicity of oxygen? |
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Effects of pH on microbial growth |
pH affects macromolecule structures and transmembrane electrochemical gradients. Each microbe will have an optimal pH range for growth. • Acidophiles = pH < 5.5 • Neutrophiles = pH 5.5 to 8.5 • Alkalophiles = pH > 8.5 |
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Effects of osmotic pressure and water availability on microbial growth |
Water must also be available for biochemical reactions (measured as water availability or aw). • Interactions with solutes can decrease aw values. • Pure water aw = 1.0; seawater aw = 0.98; honey aw = 0.6 •Most bacteria require an aw> 0.9 |
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Effects of temperature on microbial growth |
Temperature affects macromolecular structure, membrane fluidity, and enzyme function. Different microbes have different optimal growth temperatures: |
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How can different types of microorganisms be grown in the laboratory? |
grown on solid agar plates and liquid media (broths) |
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what is a complex medium |
chemical components not specifically know, e.g. medium (agar) containing blood |
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What is defined medium |
medium with precisely defined chemical composition |
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3 types of specialized media |
Selective media allows for isolation of microbes with specific properties and inhibits others Differential media allows certain microbes to be recognized based on visual reactions in the medium (e.g., lactose fermentation of E. coli on MacConkey agar) Enriched media can be used to increase a particular population of microbes with a specific property from a mixture of cell types |
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what is a pure culture? |
only one species or strain is present |
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Unculturable bacteria: What if it won’t grow? |
Cultivation independent methods • DNA from unculturable bacteria can be amplified and sequenced by PCR... Sequences can be used to produce fluorescent probes that will bind to complementary DNA (fluorescent in situ hybridization or FISH). • Metagenomics: DNA is isolated from an environmental sample. The genetic content (DNA sequence) of all microorganisms present can be compared to those from a different sample... EVEN IF THEY CAN’T BE GROWN • Microbial consortia: Some microbes maybe too accustomed to growing with their friends and neighbors to be isolated |
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how can we measure and count microbes? Direct count. Explain |
A special slide with an etched grid can be used. – A known volume is loaded onto the grid and cells are counted under a light microscope. – Pros: Cheap, fast, easy – Cons: You can’t differentiate living vs. dead cells |
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how can we measure and count microbes? viable (living) cell counting |
• 1st, the culture is diluted • 2nd dilutions are plated (the spread plate method). • 3rd after incubation, colonies are counted. • Colony forming units (CFUs) per milliliter of initial culture is calculated by multiplying the number of colonies by the inverse of the dilution factor. If the cells are very diluted i.e. large volume a filter apparatus can concentrate the cells. |
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how can we measure and count microbes? turbidity |
Turbidity (Optical Density) A spectrophotometer sends light through a culture. If the tube is cloudy, light won’t get through the tube and strike the unit’s sensor (high absorbance). It can give a rough measure of cell density in the tube. naked eye can see turbidity at 10million per mil |
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describe four basic phases of a microbe’s growth curve in a closed (or batch) culture. |
1) Lag phase: Microbes are gearing up for steady growth. 2) Log phase: Microbes are replicating at a constant and steady exponential rate. 3) Stationary phase: Replication has either halted due to lack of nutrients and excessive wastes, or the rate of replication is now equal to the death rate. 4) Death phase: Nutrients are depleted, and waste levels are high; cells are dying at a steady exponential rate. |
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From a growth curve, one can determine: |
• Generation time: The time to double the population in the exponential phase • Growth rate: Number of generations/unit of time (inverse of the generation time) • Growth yield: The maximum population density and/or amount of cellular material produced by the culture |
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what is a continuous culture? |
nutrients are fed into a vessel at a constant rate and excess medium is drained at the same rate |
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what is a chemostat? |
flows in fresh medium and takes out some old medium/microbes to keep the culture in continuous operation- can be manipulated during the experiment |
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Physical removal of microbes by filtration |
Newer methods use nylon/Teflon filters with a pore size of 0.2 or 0.45 μm (small enough to keep out most eukaryal and bacterial cells). Viruses can be removed from liquids by ultrafiltration methods (reducing pore size 10 to 100 nm). Problems can result, though: Large particles clog filters. Ultrafiltration requires high pressure. Viscous liquids don’t filter well. |
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removal by temperature manipulation |
Heat denatures proteins and nucleic acids. – 100°C kills most microbes quickly. Autoclave adds pressure, keeping fluids from evaporating at a lower heat: pasteurization for things that cant withstand the extreme heat can also freeze things, damages cells by forming ice crystals, stop biochemical reaction |
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Using electromagnetic radiation to control microbes |
UV radiation of 260 to 280 nm wavelengths can damage DNA, forming thymine dimers. This can be exploited to control microbial growth on non-living surfaces and in water |
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Chemical methods of controlling microbes |
Disinfectants: Chemicals used on non-living surfaces to kill potentially infectious microbes. Antiseptics: Chemicals that can be used on living tissue to kill potentially infectious microbes (usually only used topically) |
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What makes a chemical a “good” microbe-killer? |
• Should kill a wide range of microbes • Shouldn’t be corrosive or overly toxic • Shouldn’t leave a residue • Shouldn’t emit fumes or smell TOO bad • Should be cheap • Should be temperature stable |
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Measuring effectiveness: what is the decimal reduction time (D value)? |
Time required to kill 90% of the target organism under specific conditions |
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allosteric regulation? |
binding of effector molecule (inhibitionor activation) |
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how did we discover that DNA was the hereditary molecule? |
Griffith experiment: could transform non-pathogenic (R) strain of streptococcus pneumoniae into pathogenic (S) strain when the two microbes were mixed together Avery MacLeod and McCarty experiment: only the mixture with DNA could do this, if you added DNAase wouldnt work Hershey-Chase experiment: radioactive phosphorus was able to enter the cell (DNA) but sulfur was not |
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is DNA structure the same accross the 3 domains of life? |
yes, but the packaging is not |
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what role does dsDNA have in chromosome structure |
the wrapping of it around the histones helps compact the chromosomes in a eukaryotic cell |
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what type of genome do archaea and bacteria possess? |
single haploid genomes
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how to bacterial chromosomes replicate? |
they have a single origin of replication (oriC) and divide through bidirectional replication DNAa protein binds to OriC |
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draw the replication bubble |
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describe the termination of DNA replication of a circular chromosomes |
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where does transcription start? what molecules are involved (eukaryotic) |
at the promoter, the RNA polymerase binds there |
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where does transcription start? what molecules are involved (bacteria) |
promoters have a conserved hexanucleotide sequence at -35 and -10 regions.. the sigma factors bind to RNA polymerase to help it find promoter, then dissociates as transcription proceeds |
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differentiate between Rho-dependent and rho-independent termination in bacteria |
dependent: a rho protein follows RNA polymerase and pops it off the DNA when it reaches termination sequence independent: the DNA sequence transcribed forms a hairpin loop structure that causes the RNA polymerase to dissociate from the DNA |
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what post-transcriptional modifications are there in eukarya? |
5' cap is added and 3' Poly(A)tail is added introns spliced out and exons joined together |
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do bacteria have introns |
no |
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what is the role of amioscyl-tRNA-synthetases? |
tRNA needs to be “charged” with its cognate aminoacid.. requires ATP |
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what does "wobble" refer to? |
the codon on the mRNA doesnt need to be an exact match to the anticodon, some other binding can occur |
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how do the ribosomes of bacteria and eukarya differ |
eukarya: small (40s) subunit and large (60s) subunit bacteria: small (30s) subunit and large (50s) subunit |
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what is the shine-dalgarno sequence in bacteria? |
the ribosome binding site on the mRNA, it helps align all the machinery to the correct location
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what does the term polycistronic mean? |
it means that (in bacteria) the mRNA can code for more than one protein |
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what does it mean for eukarya to be monocistronic? |
their mRNA usually only codes for one protein |
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what happens when ribosomes reach a stop codon? |
release factors cause the complex to come apart, releasing the new protein for folding and modification |
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what is a signal peptide? |
short protein on the N-terminus of the protein, acts as a "zip-code" to direct protein to target destination |
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why are transcription and translation coupled in bacteria and not eukarya? |
the absence of a nuclear membrane and the lack in introns and post-tranciptional modifications |
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how are 30S subunits inhibited (antibiotics) |
by aminoclycosides and tetracyclines. The tetracyclines inhibit protein synthesis by impairing the stable binding of aminoactyl-tRNA to the bacterial ribosomal A-site |
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how are 50S subunits inhibited? (antibiotics)
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macrolides are compounds that inhibit protein synthesis, such as chloamphenicol, fulsidic acid, pleuromutilins |
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know the ones form the lab I guess |
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what is allosteric modulation |
binding of an effector molecule that either makes the substrate gain or lose affinity |
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what is lactose? |
disaccharide of galactose and glucose joined by a B-1,4 linkage |
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what is Beta Galactosidase? |
an enzyme family containing lactase |
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is lactose metabolized by E.coli? |
yes |
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what does this graph show |
it shows that glucose is fully consumer before the lac operon is expressed, and then lactose starts being consumed (called diauxic growth) |
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what cues are there for the lac operon to start being expressed? |
the absence of glucose and the presence of lactose |
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lac L makes repressor that binds to operator etc |
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how do effector molecules induce transcription of the lac operon? |
they inhibit the binding of the repressor to the operator |
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what role does cAMP play in the lac operon initiation? |
it is a co-activator of CRP-cAMP complex.. when the two are joined, they can bind to the activator binding (regulatory) site on the DNA which increases the affinity of RNA polymerase for promoters -- you need it to properly metabolize lactose |
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how was it discovered that the lacL gene coded for a repressor protein? |
when you mutated it the lac operon was continually expressed, but if you added lacl plasmid, repression was restored the other mutants (O gene) didnt show a restoration of repression even after the lacL was added again |
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how does a single environmental stimulus control multiple operons? |
regulons are genes that are coordinated to respond to the same regulatory systems. The genes are located in different regions of the genome |
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what are some examples of global gene regulation |
catabolite regulation: shutdown of several systems that utilize various nutrients when glucose is present the SOS response: a multigene system for wide scale DNA repair Pho regulon: gene whose expression is regulated via the conentration of phosphate in the media |
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how are sigma factors used in global gene regulation? |
bacteria have many sigma factors to direct RNA polymerases to certain genes -- lots of genes will be regulated by a single sigma |
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what is error-prone repair? |
when an SOS signal is sensed, mass DNA repair takes place which fixes a lot of stuff but also introduces more mutations |
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what is the SOS response for |
allow a cell to recognize and respond to serious DNA damage -- turns on series of genes to do a mass repair |
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what is error prone repair system |
the system that repairs DNA damage also causes errors to occur, just less than there orgiginally were |
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how does RexA and LexA respond to DNA damage |
when DNA is damaged, RecA binds to to ssDNA and it becomes inactive. LexA is destroyed, SOS genes are expressed. Once the DNA is repaied the ssDNA is not present, RecA is inactive, and LexA represses SOS genes |
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what is quorum sensing? |
chemical signalling signal, cells release autoinducer into the environment. Detecting changes in autoinducer concentration causes regulation of gene expression |
