Test 4 Campbell – Flashcards
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| What is the diauxic growth curve? |
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| There are 2 lag phases. The first one is preparing the first food source, then the second lag phase is for the bacteria to change machinery to prepare for the second food source |
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| What is an operon? |
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| Groups of genes that occur one after another and put onto the same messenger RNA. It has a promoter which helps transcription and an operator which makes the enzyme "go" |
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| What are the two types of proteins that affect regulation? |
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| Repression and Activators |
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| What is repression the repression protein? |
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| A repressor protein would be inhibiting the transcription. This binds to the operator. |
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| What is induction for the repression protein? |
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| It causes the gene to turn on. The inductor turns off the repressor. The inducer binds the allosteric site which changes the shape. The repressor therefore cannot bind and transcription can occur |
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| What is corepression? |
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| a corepressor binds to the allosteric site of the repressor, activating it to bind the operator |
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| What is the activation protein? |
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| It is a protein that promotes transcription. There is a binding site for the activator just ahead of the promoter. this will assist the sigma factors and polymerase binding the DNA. |
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| What is induction for the activation protein? |
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| Activators that need inducers will be the wrong shape to bind the binding site until the inducer comes along to bind the activator which changes it binding site to fit. |
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| What is repression of an activator? |
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| Allosteric inhibitor binds the activator which turns it off. This prevents transcription |
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| What is the Lac Operon? (LacZ, Lac Y, LacA, LacI) |
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| The Lac Operon has 3 genes: lac Z, lac Y, and lac A. Lac Z encodes for beta galactosidase. This cuts lactose into 2 products of glucose and galactose. Lac Y is the permease. It permits lactose into the cell. Lac A aids in the transport of lactose. LacI is the inhibitor |
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| What is the structure of the lac operon? (order) |
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| CAP site --> lac promoter --> operator --> lacZ --> lacY --> lacA --> lac terminator |
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| What happens when there is no lactose present in the lac operon? |
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| The gene will be repressed constantly. The repressor is expressed. The repressor will bind the operator and it blocks polymerase from leaving the promoter. It prevents the polymerase from binding. The repressor is active and the operon is off |
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| What happens where there is lactose present in the lac operon? |
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| The repressor is always on, but in the presence of lactose it needs to be taken off the operator. The lacY brings in the lactose to the cell. Induction needs to occurs. Due to chance, the repressor occasionally falls of and the message is copied. This means the cell has very small amounts of beta galactosidase. This small amount is enough to make allolactose. This is the inducer. LacZ, LacY, and LacA are all needed to bring in lactose and break it down |
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| What is catabolite repression with the lac operon? |
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| The CAP deals a lot with cyclic AMP. CAP activates the lac operon but if glucose is around, the lac operon is not needed. The glucose levels control when the lac operon works. Cyclic AMP is a signal to tell the cell how much glucose is present. Whenever glucose levels are high,cyclic AMP levels are low. Vice Versa. Cyclic AMP is the inducer for CAP so if there is no cyclic AMP, there is no CAP. If there is no glucose (high levels of cyclic amp), the CAP can turn on and there is an active lac operon. |
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| What if there is glucose but no lactose? |
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| Since glucose levels are high, this means cyclic AMP levels are low. This means the CAP is off. This means the lac operon is off as well. The repressor stays bound due to no allolactose. |
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| What if there is both lactose and glucose? |
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| Since glucose still exists, the CAP is off due to low cyclic AMP. The repressor has been induced due to lactose being present, but the helix cannot bind because there is no activator. |
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| What if there is no lactose or glucose? |
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| There are high levels are cyclic AMP due to no glucose, but since there is no lactose, the repressor is still on. Transcription cannot occur |
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| What if there is lactose but no glucose? |
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| The CAP would be active due to high cyclic AMP levels. CAP would activate the lac operon. The repressor has been induced by allolactose. Transcription occurs |
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| What is the tryptophan repressor? |
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| It is a corepressor that has enzymes to make amino acids. If the levels are low, it will transcribe. If the levels are high, tryptophan corepresses it own repressor. This is an example of feedback inhibition |
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| What is the arabinose operon? |
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| It is regulated by the presence of arabinose. If arabinose is not present, the gene will not be made to break it down. When there is no arabinose aroumd, there are special DNA binding proteins that exclude the CAP site by bending DNA. If arabinose is present, it will interact with the proteins and the strand will open. An activator is then able to be put into the CAP site. |
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| What is attenuation? |
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| It couples to translation. The amount of tryptophan in the environment affects the speed that the ribosome moves. You can then control how long parts of mRNA are free. If trypotphan levels are low, you wait longer. This is enough time for the 2 portion to pair with the 3 portion. This is an antiterminator. The ribosome will then be able to make tryptophan. If tryptophan levels are high, the ribosome is moving faster. There is not enough time for 2 to pair with 3. But 3 pairs to 4. This forms the terminator loop. The ribosome then hits that and falls apart. No tryptophan is made. |
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| What are small or noncoding RNA's |
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| They will never make proteins and are antisense RNA's. These small RNA's can base pair with mRNA's creating double stranded RNA. This creates RNA interference. This targets the message for destruction. |
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| What is Quorum Sensing? |
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| bacteria can detect how many other cells are nearby. Autoinducers are used to communicate and diffuse through the membrane easily. Gm negative cells produce AHL and Gm positive cells produce short peptides. All cells make it and there is monitoring of the levels. |
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| What is quorum sensing in V.fischeri specifically? |
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| An activator called LuxR is generally inactive until it comes into contact with its auto inductor of AHL. When the activator meets with the inductor, it binds the activator site. The RN polymerase can recruit and genes can be made. This makes more AHL. The more AHL that is made, the more the other cells take in. |
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| Where are resistance mechanisms normally found? |
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| On plasmids because they are expensive to maintain, so the bacteria will only hold on to them if they are being used |
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| What are the two types of gene transfer? |
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| Horizontal- something changes within the cell Vertical- something happens to move the genetic information to a new generation |
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| What is conjugation? |
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| Transfer is mediated by a plasmid. Cell to Cell contact is necessary. The structure responsible for this is the pilus. DNA is coming from a donor cell (F+) to a recipient cell (F-). The donor has the plasmid the recipient wants. Once the recipient recieves the plasmid, it is considered F+. |
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| What are the different fertility factors in conjugation? |
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| A plasmid in a cell is called F+. A cell without the plasmid is F-. If a F+ plasmid integrates into the chromosome, it is Hfr. It is still considered F- due to it not fuly transmitting. If the plasmid from Hfr pops out and tkaes some bacterial DNA, it becomes F'. |
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| What is a Hfr strain? |
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| When a F+ plasmid integrates into the bacterial chromosome. This makes transfer difficult |
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| What happens if an Hfr strain decides to transfer? |
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| The OriT is targeted and the plasmid has to replicate. This is difficult because the plasmid has been integrated onto a large chromosome and the entire thing needs to replicate. This is very unlikely, so most of the time, part of the plasmid and part of the chromosome get replicated and some genes can still get transferred. If the entire chromosome does not get transferred, it is still considered F- because the fertility factor is not transferred. |
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| Describe the Griffith experiment |
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| Fred Griffith discovered transformation by using encapsulated s. pneumoniae. If the outside is smooth it is diseased, if it is rough, there is no disease. He gave rough DNA to a mouse and saw the mouse did not get sick. He gave smooth DNA to the mouse and the mouse died. He killed the smooth DNA and gave it to the mouse and the mouth lived. He gave dead smooth DNA and living rough DNA to the mouse and the mouse died. When the bacteria was extracted from the mouse it was smooth. The living bacteria took the DNA of the smooth bacteria and capsulated. |
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| What is transformation? |
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| The bacterial uptake of naked DNA. Dead cell releases DNA fragments --> DNA fragment is taken up by living cell --> DNA is incorporated by homologous recombination --> cell contains new DNA |
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| Why is artificial transformation important? |
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| Competence is not done by a lot of bacteria naturally. Competence is the state of the cell wall and membrane transport a large DNA molecule. |
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| What are the two types of artificial transformation? |
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| Chemical Treatment: certain chemicals are added to the cell to weaken the membrane. This makes it easier for things to pass across. Electroporation- electricity is shot through the cell which makes holes. This makes DNA able to go through. The holes will heal but too many holes can kill the cell |
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| How does natural transformation work? |
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| It is thought to have something to do with quorum sensing. There are a lot of bacteria in lid-late log phase so this occurs so the bacteria find anything they can to survive. |
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| What does the DNA transport system look like? (Gm+) |
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| The first thing that occurs is a channel is made. ComGC makes the channel through the peptidoglycan by pilin protein. Com EA is the binding protein that positions the DNA to go through the channel. The double helix is too big to fit through the lipid bilayer, so one strand goes in by the degradation of DNa though N (nuclease). ComEC is the channel through the cell membrane. ComFA is the translocase that assists in moving the DNA through the cytoplasm. It pulls it through the entire channel |
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| What is the difference between the DNA transport system in Gm+ bacteria and Gm- bacteria? |
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| Most of the structure is the same but Gm- bacteria need an additional channel. PilQ is the channel through the outer membrane. |
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| What is transduction? |
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| DNA is transferred through bacteriophage from donor to recipient. Bacteriophages are viruses of bacteria. The virus is the donor and the bacteria is the recipient. This involves the life cycle of the bacteriophage |
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| What is a lytic cycle? |
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| This is an active cycle. It is making copies of itself and it can lyse and kill the hose cell |
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| What is a lysogenic cycle? |
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| virsus can "hide" by incorporating their own DNA into the host's chromosome. When this happens, we say they are latent prophage. A temperate phage is not actively causing disease yet but has potential to go lytic at any time |
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| What is the transduction process? |
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| There is bacteria that is getting infected by a phage. Once the DNA is inside the cell, there are 2 options. The virus can go lytic and make lots of copies, then break the cell and infect more cells, or it can go lysogenic. It will go lysogenic due to the incorrect conditions. The DNA will integrate into the host chromosome and wait. Every time the cell divides, the viral DNA goes with it. Then eventually the environment may trigger the virus to pop out and transition to the lytic phase. |
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| What is generalized transduction? |
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| This occurs during the lytic cycle. Any DNA can be transferred. the phage infects the bacterial cell and the host DNA is hydrolyzed into pieces and phage DNA and proteins are made. The phages assemble and occasionally a phage carries a piece of the host cell chromosome. Transucing phage injects its DNA into a new recipient cell. If host cell is delivered, the bacteria gains a new trick |
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| What is specialized transduction? |
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| The phages that have been lysogenic have become lytic. Only a specific portion of the host genome can be transferred. The portion on either side of where the virus is integrated can be transferred. When the virus goes the pull away from the host cell, some of the host comes with it. This can then be packaged with the phages and shipped out as well. If some host cell is given to another cell, it gains a new trick |
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| What is the merozygote? |
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| The intermediate where the new DNA is in the cell |
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| What is stable vertical transfer? |
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| If the integration of the exogenote results in replication and if the replication results in reproduction |
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| What is unstable vertical transfer? |
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| If the exogenote cannot self replication, the recipient reproduces and the exogenote cannote. Also, if the host restricts the exogenote, the exogenote does not replicate while the recipient does |
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| What are transposons? |
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| Jumping Genes. they are genes that can get out of DNA and jump back in, moving within the same cell. They can be transferred into other bacterial cells. |
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| What is the structure of a transposon? |
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| Insertion sequence. These consist of 2 inverted repeats. This means they are going to be read the same way backwards and forwards on the complementary strand. An enzyme facilitates the gene and is pulled out of the chromosome, this enzyme also helps reinsert it |
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| What is simple transposition? |
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| Nonreplicative- the jumping gene does not copy itself to be up onto another genome. Once it is pulled off the gene, the space closes up and the gene is placed on the plasmid |
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| What is a composite transposon? |
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| If a transposon has a group of genes in addition to transposase. these do not need to be contained within two inverted repeats |
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| What is the significance of transposon? |
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| They are huge sources of antibiotic resistance. They can be used to study gene inactivation |
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| What is the definition of taxonomy? |
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| The science of classification. It means to classify and give an arrangement that makes sense. |
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| What part of a bacterial name changes as new information is obtained? |
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| The genus name changes, not the species name. |
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| What is a species? |
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| A group that has the same characteristics for each other. The characteristics are very specific |
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| What are some difficulties associated with the field of taxonomy? |
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| 1. The field of taxonomy must change as new information about organisms are obtained 2. How much diversity is accepted into each group3. The use of common names are confusing compared to proper names |
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| What are the different type of strains? |
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| Biovers: differs in the structure or metabolism Serovars: differs in antigenic characteristics |
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| What are some methods in classification and identification? |
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| Phenotype, Genotype, and evolutionary relatedness based on phenotype and genotype |
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| What is natural classification? |
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| Arranges organisms into groups whose members share many characteristics. This does not work with microbes |
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| What is phenetic (artificial) classification? |
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| Organsims with similar phenotypic characteristics are grouped together. This may not provide evolutionary relatedness for prokaryotes. All characteristics are weighed equally (disadvantage) |
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| What did carl woose do? |
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| He proposed to compare ribosomes rather than DNA or RNA because ribosomes have the same structure throughout eukaryotes, prokaryotes, etc. Ribosomes function the same way in every cell, it is critical for protein synthesis, it is slow evolution, there is no evidence of horizontal gene transfer |
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| What are invariable regions? |
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| Invariable regions are regions that presume the common ancestors contain identical sequences |
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| What are variable regions? |
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| regions that are different. Oftentimes, you will see 2 closely relates organisms that contain more similar sequences in variable region |
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| What are oligonucleotide signature sequences? |
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| This sequence is organism specific. This is how groups are make from the tree of life. It is made up of 16S rRNA sequences |
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| What is nucleotide base composition? |
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| This is done from the perspective of the G+C content. The equation for percent GC is mol%GC= (G+C+A+T)*100. You can figure this out by exploiting the bond difference. This is normally determined from the melting temperature because triple bonds do not break as easily as double bonds. Each species has a specific fixed GC, family differences typically range betwenn 10%. You can only use this method to eliminate, not make a determination |
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| What is nucleic acid hybridization? |
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| The DNA of a known bacteria is separated into different strands and then a filter was put on. A second unknown organism is cut up and denatures. The second organism's DNA is attempted to bind to the DNA bound to the filter. Where it binds, it becomes radio active. The readioactivity determines the posibility of bacterial similarity. If there is 25% binding, they are probably from the same genus, if there 70-100% binding, it is likely the same species. This method is more accurate than %GC but still cannot determine identity |
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| What is the criteria for defining a species? |
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| If the bacteria shares more than 97% of their RNA sequence, if it contains more than 70% genomic hydribization, and GC, fatty acid analysis, and phenotypic methods are also considered |
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| What is RFLP? |
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| Stands for restriction fragment length polymorphism. Restriction enzymes act like scissors that cut DNA in a specific way. This helps characterize and identify strains. |
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| What is the process of RFLP? |
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| 1. Digest DNA with restriction endonucleases. The amount of cuts are equal to the number of strands since the dna is circular. 2. Pulse field electrophoresis lets us deal with large fragments. When the gels run they use electrical currents to repeal and attract DNA. This causes the base pairs to separate. If the electricity runs too long, the gel will melt, so instead there is a large pulse of high electricity. |
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| What is PCR? |
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| PCR makes methods like southern blot and RFLP easier by targeting the entire genome. The purpose is to make millions of copies to be able to be seen in a gel. |
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| What is the process of PCR? |
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| 1. The DNA is denatured at 92 degrees to seperate the strands so primers can come in 2. DNA is cooled to 58 degrees. The primers bind at this temperature, called the anneal step. 3. The temperature is raise to 72 degrees. This is the extend step which activates the polymerase, which makes a copy. |
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| What is southern blotting? |
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| This is designed to test for DNA. The bacteria is isolated and digested with restriction enzymes. The DNA is seperated using electrophoresis. The DNA is denatured to seperate the strands which are put into a filter. A radioactive probe is added to the filter which is specfic for certain parts of DNA. This allows specific strands to be tested for |
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| What is serology testing? |
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| Serology is a science that studies Ab and Ag interactions "in vitro". Antigens are Ag and antibodies are Ab. Antibodies can be made in the lab using rats and other animals which can be useful in detecting the presence of a bacteria down to the strain level |
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| What are the different types of serotyping? |
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| Indirect: The bacteria is put onto a side. The antibody is added to the smear and if it matches it will bind. Another antibody is added with flourescens. If the bacteria lights up it is a positive identification. Direct: The antibody that binds the antigen also carries the fluorescent probe. This is more expensive. |
