Mirco Test 3 Picking – Flashcards
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| Why is DNA more stable than RNA |
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| OH Group |
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| DNA Makeup |
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| Adenine, Guanine, Cytosine, Thymine |
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| RNA Makeup |
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| Adenine, Guanine, Cytosine, Uracil |
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| Backbone in DNA |
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| DeoxyRibose - Sugars and phosphate joined by ester bonds |
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| Backbone in RNA |
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| Alternating Phosphate and Ribose |
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| Purines |
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| Adenine and Guanine |
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| Pyrimidine |
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| Cytosine and Uracil |
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| Nucleic Acid polarity |
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| 5' to 3' 3' to 5' |
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| Base Pairing |
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| A-T (U) and G-C |
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| Supercoiling |
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| Allows to DNA to be "packed" into cell. Topoisomerases create and relive supercoils as well as regulate them. |
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| Replication |
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| Copies information from one strand to a new, complementary strand. |
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| oriC |
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| Point where replication begins. Replication moves from a 5' to 3'. |
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| DNA Helicase |
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| Melts and unwinds strands of DNA. Also recruits Primase. |
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| Primase |
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| Begins replication. RNA primer forms 3'Oh for DNA to attach. There is one per okazaki fragment. |
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| DNA Polymerase III |
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| Is recruited to each strand. Polymerase Synthesizes 5' to 3' on each strand. Main replication polymerase. |
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| RNase H |
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| Removes primers. |
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| DNA Polymerase I |
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| Fill gap in DNA strand. |
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| DNA ligase |
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| Seals nicks in strands. |
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| Where do new bases always occur |
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| 3' -OH |
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| Where does energy for base addition come from. |
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| Phosphate groups of the new nucleotide triphosphate being added to the strand. |
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| Leading vs Lagging Strand |
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| Leading strand is continuous. Lagging strand is discontinues, and will be or is composed of okazaki fragments. |
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| Plasmids |
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| Extrachromosomal pieces of DNA. Advantages = Specilized tasks like metoblism of rare food sources, Antibiotic-resistance genes, resistance to toxic materials, ect. |
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| High copy vs Low copy number plasmids |
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| Low copy number - one or two copies per cell, segregate similarly to chromosomes. High Copy Number plasmids - Up to fifty copies per cell, divide continuously, randomly segregate to daughter cells. |
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| Transcription (General) |
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| Creates complementary RNA structure. Has three steps initiation, elongation, and termination. |
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| Transcription Initiation |
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| Initiation - Bind polymerizing machine, first monomer to template - DNA polymerase, RNA polymerase, Ribosomes. |
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| Transcription Elongation |
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| Elongation - Core polymerase adds RNA to 3' end. Added bases are always complementary. |
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| Transcription Termination |
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| Termination - Pause at stem loop structure bound by RHO protein causes row dependent termination. Stem loop followed by UUUU sequence causes termination. |
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| RNA Polymerase I |
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| Large molecular machine; has 4 protein subunits + sigma factor which binds to DNA and reads sequence. |
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| Sigma factor (RNA Poly) * Check |
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| Smaller proteins (more than 1 type) that guides RNA poly I to site on DNA; dictates where the RNA binds. RNA polymerase binds promoter 10 and 35 bases pair upstream of start site where poly starts the unwinding and sigma factor is released. |
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| Start Codon |
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| AUG (Methionine)- Always starts protein synthesis. |
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| Stop Codon |
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| RBS codon |
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| tRNA |
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| Very stable. Carriers amino acid to new protein made in ribosome. |
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| rRNA |
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| Enzyme for protein synthesis (RNA and Enzyme) - Ribosomal RNA. |
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| Anticodon loop |
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| base pairs found on tRNA that correspond to the mRNA. |
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| aminoacyl-stem |
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| Stem on tRNA loop where amino acid can bind. |
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| rRNA A site |
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| Where incoming tRNA carrying an amino acid binds on the ribosome |
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| mRNA P Site |
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| where the tRNA that has the growing protein is bound on the ribosome |
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| mRNA E Site |
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| where the empty tRNA that is about to be ejected is bound on the ribosome. |
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| Monocistronic mRNA versus polycistronic mRNA |
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| Wether or not a mRNA has more than one binding site for protein creation. |
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| Horizontal transfer |
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| Transfer of large genetic material from cell to cell without being spawn. |
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| Transformation |
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| Up take of "naked" DNA from enviroment |
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| Conjugation |
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| Bacterial "sex". Pillus is appendage used for transfer. F plasmid is code that enables cell to have/use pillus. F+ is the male giving cell, and F- is female receiving cell which will form and F plasmid. |
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| HFR |
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| High frequency recombination - F Factor integrates on bacterial chromosome and tries to transfer entire chromosome. |
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| Transduction |
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| Viruses inject DNA, then bacteriaphage can transfer DNA to another cell from host. |
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| Restriction endonuclease |
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| Protection against foreign DNA. Cuts DNA that enters cell unless it has been methylated at specific cut sites. |
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| Vertical Transfer |
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| Transfer of material through ancestry. |
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| Point mutations |
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| Change a single base pair.http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/M/Mutations.html#silent
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| Silent mutation (point) |
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| No affect on cell but affect on genotype. |
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| Missense Mutation |
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| Variable affect on the cell. CGA -> CAA |
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| Nonsense mutation |
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| Changes a codon to stop. total affect dependent upon how close to the end of the strand the mutation occurs. |
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| Frameshit mutation |
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| insert or deletes a single base which alters all of the downstream codons. usually results in drastic changes. |
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| Ames Test |
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| Test using salmonella and the bacterias ability to make histidine. Used to identify compounds that are mutagens based on the compounds ability to cause reversion. |
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| Exision repair |
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| type of repair used to repair crosslinked thymidine dimers. Low risk,cut out the sequence with DNA poly 1 based on the other stands sequence. |
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| SOS Repair |
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| High risk. uses RecA, induced when there is so much damage to the cell that it is unlikely to survive. Last Ditch effort. Error prone. May mean replacement with other parts of chromosomes. |
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| Transposable elements (transponsons) |
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| Transposons are jumping genes that move around the genome causing mutations. |
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| How do bacterial cells sense the environment. |
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| Two component signal transduction. Sensor kinase protein binds to signal, hunts food, uses chemical cues. Cytoplasmic response regulator takes phosphate from sensor and binds to the chromosome to alter transcription rates of genes. |
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| Regulating transcription |
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| Sigma factor guides RNA polymerase to initiate transcription at promoter. Activator binds DNA sites to next promoter and increase frequency of that genes transcription. Repressor binds to DNA site on top of promoter and lowers frequency of that genes transcription. |
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| LacOperon |
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| Enables utilization of lactose as a food source, Beta-galactosidase breaks down lactose into glucose and galactose. |
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| LacOperon promoter binds using |
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| Sigma factor binding. |
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| Lac Operon operator |
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| DNA sequence where lactose repressor LacL binds. Overlaps with promoter. |
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| Lac Operon Inducer |
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| Lactose or allolactose - Binds to repressor to cause it to fall of the operator. |
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| Catabolite repression |
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| Glucose effect on cAMP levels - high glucose means low cAMP, low glucose means high cAMP. |
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| Replication Steps |
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| 1st - Unwind DNA with helicase 2nd - primer is made from primase 3rd - DNA poly III starts making DNA 4th - Get rid of primer with RNase 5th - Fill in nics with DNA poly (?????) |
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| Virus vs viroid versus prion |
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| Virus has small genome (DNA or RNA) encapsulated in a protein. Viroid is RNA only usually plant pathogen. Prion is misfolded protein. |
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| Filamentous capsid |
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| Long tube of protein with genome in side. Tube is made up of hundreds of identical protein subunits. |
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| Icosahedral capsids |
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| 20 triangular sides, with each triangle being made up of at least 3 identical capsid proteins. |
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| Complex capsids |
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| Mixture of icosahedral and filamentous shapes. Many bacteriaphages have this form. |
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| Envelopes |
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| Membrane that surrounds capsid produced by host cell. Only produced by hosts who do not have cell wall. |
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| SS+ RNA Virus |
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| Can be translated directly by host ribosomes. One of first proteins translated will be replicase or RNA-dependant RNA polymerase |
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| SS- RNA virus |
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| (must carry their own replicase enzyme) can’t be translated by ribosome so it must carry its replicase with it (must make a + strand for protein translation and to serve as a template for make – strand genomes |
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| DS RNA virus |
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| one of the strands can be translated directly, but it usually carries its replicase with it |
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| Retrovirus |
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| + Strand single strand RNA + reverse transcription into DNA |
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| SS DNA Virus |
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| Parvoviruses. Carries its on Polymerase. |
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| DS DNA virus |
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| Pox viruses |
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| Typical Virus Life Cycle |
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| 1. Attach to host cell 2. Get viral genome into host cell 3. Replicate genome 4. make viral proteins 5. assemble capsids 6. Release progeny viruses from host cell |
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| Bacteriophage life cycles (Lytic) |
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| Kills host, follows same typical virus cycle. |
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| Lysogenic |
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| integrates into host chromosome until SOS response is initiated – then it begins the lytic cycle |
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| Example of a + ss RNA lytic virus life cycle |
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| Polio virus, makes poly protein |
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| Example of a ds DNA lysogenic life cycle |
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| Lamda Phage |
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| Example of retrovirus lifecycle |
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| buds off (enveloped) so makes for a long slow disease process that (for HIV) affects immune system cells |
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| Stages of virus growth when culturing them |
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| 1. Eclipse - after entry/uncoating, no noticeable viruses 2. Rise - Begin to see viruses 3. Burst - the number of viruses released per host cell upon lysis of the host cell |
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| Budding |
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| How animal enveloped animal viruses gain their envelope |
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| Plaque |
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| a whole in a lawn of bacteria caused by their lysis by phages |
