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135 Cards in this Set
- Front
- Back
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Which element is required in minute amounts in microbiological media?
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manganese
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What is the function of siderophores?
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Binding iron for transport into the cell.
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Autotroph uses (blank1) as a source of (blank 2)
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carbon dioxide; carbon
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Heterotrophs use (blank) as a source of (blank)
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organic compounds; energy
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What is nitrogen fixation?
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Reduction of DINITROGEN to AMMONIA for assimilation
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Most common solidifying agent used in microbiological media?
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Agar
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bacterium that have an absolute requirement of oxygen for growth.
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aerobe
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Enzyme catalyse used to detoxify which harmful oxygen species?
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hydrogen peroxide
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Microbes that grow optimally at a pH below 5.5
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acidophiles
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Microbes that grow at very high salt concentrations
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halophiles
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A method used to obtain a viable cell count
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Plate counts for serial dilutions
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Used to measure the optical density of a bacterial culture?
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spectrophotometer
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The plate count method was used to estimate the number of bacteria in a culture over time. Serial dilutions were made of culture samples at various time points. A 0.1 ml portion of the 10-6 dilution was spread over the surface of a nutrient agar plate for each time point. The plates were incubated for 24 hrs and the colony forming units (CFU) were counted on each plate. A total of 45 colonies were counted on the plate for the 30 minute time point. What was the cell population for this time point?
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45x10^7
question 24, ch. 6 |
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Fresh media is inoculated with an actively growing Escherichia coli culture. You measure the optical density (OD) at the time of inoculation and record avalue of of 0.05) Two hours later you take another reading and record a optical density of 0.2) What is the generation time for your culture?
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ch. 6 question 26
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How long would it take a culture of E. coli with a starting cell density of 1 X 105 cells/ ml to reach a cell density of 1 X 108 cells/ml if it had a generation time of 30 minutes?
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5 hours, ch. 6 question 29
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What is chemostat?
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A system used for the continuous culture of microbial cells.
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During steady state growth in a chemostat, the growth rate of the cells is equivalent to...
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the dilution rate
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method for the sterilzaiton of an environmental water sample?
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autoclaving the sample
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define antiseptic
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A chemical agent that is applied to living tissue to kill and inhibit microbes
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How does ehtanol and isoproanol reduce bacterial load?
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disrupting the bacterias plasma membrane.
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Example of an oxidizing agent
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chlorine bleach
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Pharmaceutical products that are heat sensitive are sterilized by...
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ionizing radiation
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Experiment by Fred Griffith with R and S strains of Streptococcus pneumoniae demonstrated...
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Genetic material from one strain could be transferred to another strain.
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The experiment by Avery, MacLeod, and McCarty with R and S strains of Streptococcus pneumoniae demonstrated...
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DNA was the genetic material in cells.
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The Hershey and Chase experiment distinguished that DNA, not protein, was the genetic material in cells. The discernible feature between them is that (blank) is incorporated into DNA while (blank) is incorporated into proteins
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phosphorous; sulfur
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What do microorganisms need to grow?
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large amounts of carbon, nitrogen, phosphorous, sulfur, and oxygen.
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organisms with a chemical energy source
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chemotroph
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organisms with a light energy source
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phototroph
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organisms with an organic electron source
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organotroph
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organisms with n inorganic electron source
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lithotrophs
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organisms with an organic carbon source
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heterotroph
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organisms with an inorganic carbon source
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autotroph
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A category for an organism that has...
a chemical energy source an organic electron source and organic carbon source |
chemoorganoheterotroph
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What is a common form of nitrogen?
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Ammonia
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Prototrophs
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syntehsize all needed marcomolecular precursors from a single carbon source and inorganic molecule.
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Auxotrophs
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cannot synthesize all the needed precursors from a single carbon source.
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What is a limiting factor for microbial growth?
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one key nutrient, available in the lowest amount, will dictate how much growth can occur over time.
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obligate aerobes
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require oxygen
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obligate anaerobes
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cannot grow when oxygen is present
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facultative anaerobes
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can use oxygen but can also grow in the absence of oxygen.
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aerobes produce how many atp?
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36
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anaerobes produce how many ATP
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2
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how does pH affect protein
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pH affects the fold of protein, which will determine the shape and function; thus, directly influencing where and when cells will grow.
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Media for microbial growth can be either complex or defined. Define these two terms.
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Defined: growth rates are very slow, know everything in there and it is pretty cheap.
Complex: things grow fast, expensive, composition is unknown. |
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Why are complex growth (for microbial growths) unknown?
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The growths contain peptone and yeast extract.
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What is the rule of thumb for overnight cultures?
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You will need to dilute the culture to get single colonies so a culture containing 10^9 cells should be diluted 10^7 times to get a descent number of colonies to count.
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Metagenomics
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Genetic content of microorganisms in one area can be examined and compared to those of a different area
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When measuring and counting microbes there are several different methods. How is the turbidity measurements utilized for cell measurement?
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There is a linear relationship between the light going through and the number of cells you have.
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Direct counts: Petroff-Hausser counting chamber
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volume is loaded onto a grid and cells are counted.
Pro: cheap, fast, easy cons: you can't differentiate living vs. dead cells. |
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How many cells in an overnight culture?
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10^9 cells/ml
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How do you find the dilution of cells?
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Take the average: 85 cells
Density: 85 cells/L convert to mL = 850 cells/mL Dilution: (850 cells/ml)*10^2 = 85,000 cells/mL |
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What does a spectrophotometer do?
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it sends light through a culture.
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What is D-value
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the amount of time to kill 90% of something.
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Pasteruization is...
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low-temperature heating to reduce microbe numbers
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What is the temp. and time a person should put an organism in an autoclave to kill microbes quickly?
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121C for at least 15 minutes
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What is the benefit of nylon filters for microbial filtration?
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prevents bacteria from getting into the solution (0.2 um filter) will make the solution sterile.
IT DOES NOT REMOVE VIRUSES. |
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What is chemostat?
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flows in fresh medium to take out old microbes and keep the culture in continuous operation.
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Name the four phases of microbial growth
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lag phase
log phase stationary phase death phase |
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explain lag phase
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microbes are getting ready for steady growth
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explain log phase
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microbes are replication at a constant rate and steady exponential rate
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stationary pahse
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replication has either halted due to lack of nutrients and excessive wastes or the rate of replication is now equal to the death rate
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explain death phase
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nutrients are depleted and waste levels are high; cells are dying at a steady exponential rate.
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How do we know that DNA is a hereditary molecule?
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The Griffith Experiment.
Avery, MacLeod, and McCarty experiment Hershey-Chase experiment |
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What is the griffith experiment?
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One of the earliest experiments that pointed out that DNA could contribute hereditary info in bacteria using S and R strains of pneumoniae.
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Explain the results of Griffith's experiment (what rat died from what train and so on).
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Injecting rats with smooth pneumoniae was deadly
Rought strep. pneumoniae was not deadly. Smooth could be harmlessa by heating the strain for 121C for 15 minutes. |
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what is the Avery, MacLeod, and McCarty experiment?
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Using Griffith's experiment, saw that DNA left over could transform from R cells to S cells. Which meant that DNA was the molecule for transformation.
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What is the Hershey-Chase experiment?
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Allowed phages to infect bacterial cells (these were proteins and DNA to see if if there was some protein or RNA that were creating the Avery transformation results). The only phage in the bacterial cells was DNA which proved that protein was not the hereditary molecule but DNA.
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What did Franklin, Watson, and Crick elucidate?
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The double-stranded double helix structure of DNA.
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Name the nucleotide pairings and their # of H bonds
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A and T with a double hydrogen bond
G and C with a triple Hydrogen bond |
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What the backbone of each DNA strand?
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Phosphodiester covalent bonds form the sugar/phosphate backbone.
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Describe the chromosome shape of:
Bacteria Arachaea Eukarya |
Bacteria: single, circular chromosome
Archaea: single circular chromosome around histone proteins. Eukarya: multiple linear chromosomes packaged around histone proteins. |
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What's the size of a single gene?
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1000 nucleotides
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average size of bacterium?
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.5-5um
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what compacts the chromosomes of eukaryotic cells?
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wrapping dsDNA around the histones of eukaryotic cells packs the chromosomes more tightly.
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D. radiodurans (a bacteria) is characterized by its incredible resistance to radioactivity. Why this resistance?
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Because it is 4-10 chromosomes stacked on one another which allows it to withstand radioactivity because of the multiple copies.
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what is a semi-conservative process and why is DNA replication characterized as such?
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Each time the dsDNA is copied, each copy carries one strand of the original molecule and one newly-made strand.
The original has been "semi-conserved" |
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T/F DNA has to be unwound before replication.
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true
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What section of the DNA strand can polymerization occur? (for initiation and elongation)
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at the 3' prime.
Laggins strand is pieced together and placed (pieced via okiazaki fragments) but he leading strand does not need to be pieced. |
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gaps from the okizaki fragments (initiation and elongation) are filled with what?
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new nucleotides before DNA ligase seals the backbone.
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What is a gene?
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a segment of DNA that gets copied (Transcribed) into ssRNA.
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Explain transcription of DNA in BACTERIA
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RNA pol separates DNA and lays the complementary strand of RNA. (always)
Sigma factors bind the RNA pol core enzyme and direct the combined holoenzyme to a promoter - when RNA pol is situated the sigma factor dissociates and transcription continues. |
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Termination in transcription in bacteria
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Rho-dependent!
rho proteins follows RNA pol and pops them off the DNA. Rho-independent: DNA sequence forms an RNA hairpin loop that causes the RNA pol to dissociate from the DNA. |
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Eukaryal transcription termination is dependent on the RNA pol, but the modification after transcription remains the same across all three pols. Explain it.
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a 5' cap is added.
Poly(A) tail added INTRON are spliced OUT and Exons join together. |
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Explain translation.
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ribosomes interact with mRNA and tRNA that is charged with a particular AA. Each codon (nucleotide triplet) matches a complementary anticodon on the tRNA molecule. The peptide bond forms between whatever amino acids are delivered.
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What are the three stop codons in translation?
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UAA
UAG UGA |
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What is "wobble?"
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a phenomenon characterized by no needing an exact match to the anticodon - allows 61 codons to code for insertion of 20 AA into proteins.
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Before translation can occur what must happen to the tRNA?
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it must be charged with whatever AA it has to bring to the ribosome.
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what are chaperonins?
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Occurs during translation.
Assist in correct folding/refolding of polypeptide sequences. |
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The possible affect of DNA replication error is mutation. What is the results?
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they can alter the coding portion of a gene, resulting in a protein functioning in a completely different way than initially intentioned.
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Name the types of mutations
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Silent
Missense Nonsense (slide 52, ch7) Frameshift (53, ch7) |
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What is a silent mutation
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Usually in the third position of the codon. Results in no change in the AA sequence of the protein.
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What is a missense mutation?
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a chage in a codon that results in coding for a different AA at that position in the eventual protein.
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What is a nonsense mutation
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A change the forms a stop codon where on a stop codon shouldn't be found.
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What is a frameshift mutation
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Insertion or deletion of nucleotides. It changes how a ribosome "reads" an mRNA molecule and can dramatically alter AA sequence of proteins.
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How do viruses recognize appropriate cells?
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Interaction between viral attachment proteins and host cell receptor molecules.
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what is the receptor molecule for HIV
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CD4
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Name some of the different way a virus can attach to cells.
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Tail lands on the host and interacts with specific proteins on the cell surface.
Capsulated viral particles - proteins on the outer coat where sticking out proteins recognize proteins on the host. |
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Explain the entry of enveloped viruses (for influenza)
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Influenza
Protein on the outside will recognize a protein on the host. It will be enveloped (endocytosis) --> pH to get rid of the capsid to bind to the vacuole and release virus. |
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Entry of enveloped virus (for HIV); what is fuzeon?
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two proteins - gp120 and gp41
CD4 is crucial for our cells (important for immune response) Fuzeon - prevents the folding of gp41 to prevent the virus from entering the cells. |
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Entry of non-enveloped viruses (reovirus)
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Binding to a receptor on the cell surface triggers receptor-mediated endocytosis.
Virus is interacting with the plasma membrane. |
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Entry of bacteriophages
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Nuclear material in the head to be injected and will be
Lysogenic or lysis making copies and make more nucleic acid - lysogenic make the copies and lyse the cell - lysis |
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Entry of plant viruses
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Tough cell wall structures, plan viruses often require damage induced by insects to infect the plant cells.
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What is viral uncoating?
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The viral genome is inserted into the host cell.
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Replication of TYPICAL eukaryal DNA viruses
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Heading in for transcription and out for translation.
Goes to the nucleus to get DNA inside. Will use the host DNA polymerase to make its own DNA. |
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What is atypical replication?
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Viruses bringing their own RNA polymerase so they do not have to enter the nucleus.
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What is atypical eukaryal replication
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Brings on RNA polymerase but uses the hosts machinery.
Uses mRNA using its own enzyme --> uses the hosts ribosomes for proteins so that the viral proteins can start again. |
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Explain the replication of a positive-sense RNA virus
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they bring their own RNA-dependent RNA polymerase.
WIll make an enzyme from the hosts ribosome to make more RNa. The RNA will make more protein so it can keep itself going. |
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T/F you need the entire viral capsid for the virus to work.
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False, as long as the nucleic acid is shoved into the cell it will work.
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Explain making more RNA from original RNA
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Brings its own enzymes
has to be converted to a positive strand the virus must bring its own enzyme so that it can function (negative to positive strand) Positive strand can be converted into proteins and the RNA polymerase to make functioning virus. - More protein more nucleic material. |
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Explain the replication of retrovirsues
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RNA is converted to double stranded DNA through reverse transcriptase.
The DNA will convert to protein by going through mRNA, more RNA is made form nuclear material. Protein will decorate the outside of the capsid. |
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What is the best studied phage?
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Lambda
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What does Lambda attack?
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E. Coli
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Explain how Lambda attacks E.Coli
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Injects double-stranded DNA, becomes a circle, that circle is integrated into the chromosome of the bacteria (lysogenic phase)
it can either stay and make copies via daughter cells or lyse the bacteria. |
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How do virus particles form and exit cells?
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Assembly...viral components are self-assembling to make the process fast and "cheap".
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What is egress?
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Exit from the cell.
Enveloped PLANT VIRAL PROTEINS in the host cell plasma membrane bud out of the cell taking a portion of the plasma membrane so that it can recognize new hosts. |
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How do antiviral drugs work? what constitutes a "good" drug?
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easily administered
easily produced relatively affordable few side effects decrease severity of disease. |
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what antiviral drug is used for HIV treatment?
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AZT
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Describe AZT
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No 3' prime end.
AZT will confuse reverse transcriptase and now the virus can't make more nucleic acids thus halting its lengthening. |
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What a good example of an antiviral drug (other than AZT)
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tamiflu - prevents the activity of the enzyme that helps a new virus detach from the infected cell.
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What are auxotrophs
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nutritional mutants.
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% composition of cell that is protein
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50%
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What is reversion?
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Spontaneous mutation that "corrects" a metabolic abnormality back to the wild-type form.
Problematic when determining mutation rates. |
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How many genes make a bacteria?
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5,000
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how many nucleotides make up plasmid?
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10,000 nucleotides
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How many nucleotides make up a gene?
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1,000
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T/F plasmids put into cells have to be compatible
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True. You want plasmids that are different from one another, different by origin and replication.
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difference it gene and protein abbreviations
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Genes: three letter in italics followed by a capital letter.
Protein: three letter but with the first letter capitalized and no italics. |
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Two ways to detect mutations through the phenotype
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Selection - growth medium that wil linhibit microbes lacking the desired genes.
Screening - colony grows on a fully nutritionally supported plate but doesn't on a partially supported plate. |
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What is replica plating?
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done during phenotypic screening it is a method involving the photocopying of growths.
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What is patching?
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Transferring colonies to a gridded plate.
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Dullest experiment in the history of science
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Lenski - transfers 0.1 ml of cells to 9.9 ml of fresh medium every day.
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what did Lenski's experiment show?
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Evolution is repeatable.
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What is a restriction enzyme?
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allows cutting of specific DNA pieces.
"Enzomatic scissors". THe similar ends of cut DNA care be paired together (palindromes). |
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When DNA pieces are asymmetrically cut with enzomatic scissors, they must be pasted back together. What pastes them back together?
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Ligase which is bonded covalently
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What is the x-gal system?
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When searching for a gene - it will show blue colonies, but if there are cloned genes, the growths will be white.
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