studium 0.18.7

data/lib/studium/exam_topics/bacteriophages

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+# =========================================================================== #
+# === Bacteriophages
+#
+# (Bacteriophages tag, phages tag, virophages)
+#
+# This file keeps information about Bacteriophages. It is thus quite similar
+# to the file basic_virology, but focuses solely on phages of bacteria and
+# archaea. Phage genetics may also be stored in this file, as well as the
+# phage lambda, due to to its historic significance.
+#
+# Information that is secondary to phages, such as which genomes carry a
+# phage, may be included here as well.
+# =========================================================================== #
+
+- In a <one>density gradient of lambda particles</one>: where may we find it, compared to DNA and protein bands? About half-way since half the mass of a lambda particle is DNA and half is protein. (Density of DNA is 1.7 gm/cm3; the density of protein is 1.3 gm/cm3).
+- Do phages inactivate a critical component of the CRISPR machinery? Yes, some phages are known to do this. There ware at the least nine distinct families of anti-CRISPR proteins described, made by various phages.
+- Finden wir überlappende Gene in Phagen? <one>Ja</one>.
+- Do we know <one>a phage</one> that <two>can act as a Transposon</two>? <one>Yes</one>: the "Mu Phage". URL: ADD URL HERE.
+- For <one>phage recombination</one>: what is one important requirement for it to work? The phages that undergo recombination must be of "different genotypes".
+- <one>How long</one> does it take the T4 phage to infect a host cell until it can lyse it? <one>25 minutes</one>.
+- Beim Lambda-Genom: das Gen A + Nu1 binden woran? An <one>mm'</one>.
+- The <one>lambda phage</one> encodes about ... n different proteins? About <one>70</one>.
+- <one>How</one> can the "att sites" of lambda be defined, experimentally? Via <one>mutations</one>; mutations of these sites will prevent the integration of lambda into the bacterial genome.
+- In the lambda-phage heads the DNA is present as linear double stranded DNA, containing 12 nucleotide long cohesive ends. These ends are generated by cleavage of this DNA by ... which enzyme? By the <one>lambda terminase</one>.
+- Do <one>phages</one> make use of <two>5-hydroxymethylcytosine</two> (<three>HMC</three>)? <one>Yes</one>, <two>some do</two>.
+- The <one>lambda early stage</one> takes how many minutes? About <one>15 minutes</one>.
+- <one>Phages</one> <two>can perform</two> <three>specialized recombination</three>. Do the sequences have to be homologous in this form of recombination? No, not necessarily.
+- The <one>T4 phage</one> contains the <two>rII locus</two>. If a mutation occurs in this gene, what may we conclude? That this T4 can then no longer grow on the "E. coli strain K12".
+- <one>What transcripts</one> will be found in a "quiescent prophage"? Only <one>bacterial transcripts</one>.
+- Give <one>one example</one> for a "transposable phage". A: The <one>Mu Phage</one>.
+- Does the <one>MS2 phage</one> make use of "overlapping genes"? <one>Yes</one>: its "lysis protein" has "overlapping genes".
+- Die <one>rII Region</one> des <two>T4-Phagen</two> umfasst wieviele bp? <one>4000 bp</one>.
+- What is meant with <one>maturation</one> of a bacteriophage? This means that the viral particles assemble into a new bacteriophage.
+- What are <one>temperate phages</one>? These are <one>phages</one> that can undergo either the lytic or the lysogenic cycle. In other words: these bacteriophages can switch between the lytic and the lysogenic mode. 
+- Name the <one>two best characterized temperate phage</one>. A: (1) <one>Lambda</one> (2) <one>P1</one>
+- The <one>bacteriophages</one> can be characterized into which "behavioural categories"? Also provide one example for each category. A: (1) "temperate phage": "Lambda" (2) <one>virulent phage</one>:  <two>T4</two>
+- Give a reason as to why phage therapy was not the ultimate breakthrough that it was initially assumed to be. A: Bacteria tend to mutate towards phage-resistant forms.
+- When did d'Herelle give phages their name? In <one>1917</one>. URL: https://en.wikipedia.org/wiki/F%C3%A9lix_d%27H%C3%A9relle
+- <one>Seymour Benzer</one> began to map part of the genome of bacteriophage T4 at high resolution in the year ...? <one>1954</one>.
+- Can <one>metabolites</one> induce lysogenic prophages? Yes, via the SOS response usually.
+- Name a phage infection sensing system. A: <one>Arbitrium</one>.
+- Some bacteriophage synthesize <one>arbitrium</one>, a viral peptide. This peptide is how long? It is <one>a hexapeptide</one> - thus, it is six amino acids long.
+- Can <noe>antibiotics</one> <two>induce prophages</two>? Yes, such as mitomycin C. This often happens via the RecA-dependent SOS response.
+- Do <one>filamentous phages</one> exist? <one>Yes</one>.
+- If we read the statement <one>phage was adorned with sweetness</one>, what could be meant by that? For instance, when something is incorporated into a phage - such as DNA - that is adorned with a sugar molecule. Thus, this refers to a modification.
+- Some phages communicate using which peptide signal, in order to control the decision of entering lysogeny? <one>Arbitrium</one>.
+- Some bacteriophages can replace adenine in their genome with which non-standard nucleotide? <one>Diaminopurine</one>.
+- Do phages encode for <one>DNA methyltransferases</one>? Yes, some do.
+- Phages fear which <one>murderous enzymes</one>? The <one>restriction endonucleases</one>.
+- How are phages called that target bacterial flagella? <one>Flagellotropic phages</one>.
+- An icosahedron phage has how many vertices? <one>Twelve</one> (12).
+- The great majority of known phages that infect Bacteria make use of which capsid type? They use an <one>icosahedral capsid</one>.
+- The first phage genome was sequenced in the year ... ? <one>1977</one>.
+- Why can it be said that <one>the capsid of a phage is more than merely a a resilient shipping carton</one>? Because the capsid may also recognize a host when it collides with one.
+- The <one>M13 phage</one> contains about ... how many copies of the coat protein pIII on its surface? <one>5</one> (<two>five</two>).
+- Gibt es Bakteriophagen die für Lysozym kodieren? Ja. URL: https://de.wikipedia.org/wiki/Lysozym#Funktion_der_Lysozyme_bei_Bakteriophagen
+- The <one>lambda phage genome</one> contains n bp? <one>58 402 bp</one>.
+- In the year <one>1952</one>: Hershey and Chase used E. coli cells and which phage? The <one>T2 phage</one>. URL: https://en.wikipedia.org/wiki/Hershey%E2%80%93Chase_experiment
+- Is the <one>lambda phage</one> a contractile tailed phage? No; it is <one>non-contractile</one>.
+- Der Phage <one>Lambda</one> benutzt und besitzt Proteine mit antiterminierender Wirkung. Diese werden eingesetzt als Schalter für die frühe und späte Phase seiner Genexpression. Nenne zwei Proteine die in diese Kategorie fallen. A: (1) <one>Protein N</one> (2) <one>Protein Q</one>
+- Was ist mit der <one>Gerüstfunktion</one> gemeint bei Phagen? Dies sind Proteine, die bei der Struktur für andere Proteine wichtig sind, jedoch selbst nicht im Phagen verbleiben.
+- Welches Enzym schneidet die concatemere Lambda-DNA? an den cos-Stellen? Die <one>Terminase</one>.
+- Der Hauptbaustein des Lambda-Phagenkopfs ist welches Protein? Das <one>GenE-Protein</one>.
+- The 12 nucleotide 5' overhangs at the cos-ends of the linear <one>Lambda DNA</one> are the result of a cut by which enzyme? <one>Terminase</one>. 
+- The lambda genome contains n genes? <one>71</one>. URL: https://en.wikipedia.org/wiki/Lambda_phage
+- Is there a phage that carries a cytochrome P450 gene? Yes, the <one>Mycobacterium phage</one> called <two>Adler</two>.
+- The best documented example of a lysogenic phage conferring pathogenicity on its host is found in ... ? Corynebacterium diphtheria, the cause of diphtheria. The gene for this is carried on a lysogenic phage.
+- Der T4-Phage hat ein Protein das AsiA genannt wird. Asi steht hier für ... ? Anti-Sigman.
+- Können Bakteriophagen für Sigmafaktoren kodieren? Ja - zum Beispiel der Sigmafaktor 34, von BPSP1. URL: https://www.uniprot.org/uniprot/P06227
+- Der Phage <one>SPO1</one> benutzt welches Bakterium als Wirten? <one>Bacillus subtilis</one>.
+- Nenne eine vom <one>M13 Phagen</one> abgeleitete Labor-Technik. A: <one>Phage Display</one>.
+- Durchmesser des <one>M13-Phagen</one>? <one>9 nm</one>.
+- From the point of view of biotech-industry, why are phages not always considered to be a blessing? Because the phages may cause economic damage, where the product resulted from <one>bacterial fermentation</one>.
+- There is a satellite virus, a phage, called <one>Enterobacteria phage P4</one>. It requires, as helpfer virus, which other phage? Enterobacteria phage P2.
+- Some large phages of photosynthetic bacteria encode proteins that enhance photosynthesis. Why might this be employed? This may probably boost yields of virus from these cells in the long run.
+- Lysogens of lambda "cI 857" can be induced to switch from lysogenic to lytic mode ... how? By <one>shifting their temperature above 37 °C</one>.
+- Nenne einen Phagen mit intramolekularer Doppelstrangschleife. A: Der Bakteriophage <one>G4</one>. URL: URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0027062
+- Das <one>Genom des M13-Phagen</one> umfasst in etwa n Nukleotide? Etwa <one>8000 Nukleotide</one>.
+- <one>Bacteriophages</one> are <three>typically cultured in</three> ... ? <one>Bacterial cells</one>.
+- The <one>lambda-phage</one> belongs to which class of the "Baltimore scheme"? Lambda belongs to <one>Group I</one>, aka "dsDNA-viruses".
+- Wieviele <one>ORFs</one> hat das <two>Lambda-Genom</two>? Etwa <one>73</one>.
+- Why is <one>Lambda-Replication</one> considered to be "asymmetric"? One parental strand continues to serve as a template - the other strand is used only once.
+- Bei der Freisetzung von Lambda-Phagen aus einer bakteriellen Zelle wird oft welches Enzym benötigt? <one>Endolysin</one>.
+- Der <one>Lambda-Phage</one>: welche Infektionsstrategie wird bevorzugt wenn der Phage in einem nährstoffreichen Medium wächst, und welche molekulare Grundlage kann hierzu genannt werden? Der Lambda-Phage bevorzugt den lytischen Infektionsweg bei einer nährstoffreichen Umgebung. Ein derartiges Medium aktiviert die <one>HflB-Protease</one>.
+- Nenne die drei strukturellen Haupt-Bestandteile des <one>Lambda-Phagen Virions</one>. A: (1) <one>Kopf</one> (2) <one>Schwanz</one> (3) <one>Schwanzfaser</one>
+- Sind alle Lambda-Phagen Gene des Lambda-Genoms charakterisiert im Jahre 2019? Nein.
+- Der <one>Lambda-Phage</one> bindet woran genau an der bakteriellen Zellmembran ...? An das <one>Maltose-Porin LamB</one>.
+- Name two different, general "stress conditions" that could possibly re-activate a lambda prophage. A: (1) "DNA damage to the host", such as via "<u>UV treatment</u>" (2) "temperature upshift to 42°C", if we have a "thermosensitive allele" of the lambda repressor protein
+- Der <one>T4 Phage</one> kann auf E.coli strain B und K wachsen. Auf welchem einfacher? Auf "strain B". Bei einer Mutation im Gen rII kann T4 nicht mehr auf dem strain K wachsen.
+- Nenne einen <one>Phagen</one> der "generalized transduction" durchführt! A: Der "Phage P22".
+- If an "E. coli cell" is infected by more <one>lambda phages</one> at the same time, rather than just a few ones, will it be more likely that the lytic or lysogenic cycle will be initiated? Larger numbers of co-infecting phages make it more likely that the infection will use the "lysogenic cycle".
+- When do phages require a "<u>helper phage</u>"? When it is a "defective phage".
+- Can we say anything about the organization of a typical phage's genetic map? Yes - it will "often reflect the sequence of lytic development" of that phage.
+- If we see an E. coli culture is infected by lambda phages, and these phages synthesize lots of cro proteins, what may we conclude to happen next? The "lytic cycle" will be induced if the cro proteins dominate.
+- Why does the "bacteriophage lambda" require the "cI repressor"? This repressor is required in order to "maintain lysogenic growth".
+- How fast is the "<u>T4 phage</u>" in shutting down the bacterial cell after infection? Within "two minutes after infection", that cell will be shut down.
+- Is the "Corticovirus" icosahedral or a head-tail phage? It is "icosahedral".
+- The "bacteriophage MS2" has a central area in its genome coding for the coat; following by a lysis protei and a replicase. Which protein can we find at the beginning? The "maturation protein". URL: https://en.wikipedia.org/wiki/Bacteriophage_MS2
+- Typically bacteriophages are released from a bacterium how? Via "lysis" of the bacterium.
+- For "phage lambda", what happens if the default att-lambda site is deleted? The lambda-phage "may still establish lysogeny" by simply integrating elsewhere - with an efficiency of "less than 0.1%" compared to the default att-lambda site.
+- How does the "T4 phage" protect itself against its own nucleases? The T4 DNA contains an unusual base ("HMC": "5-hydroxymethylcytosine").
+- Why does the lambda phage require the "cIII gene product"? This protein will "protect cII" from "proteolytic degradation" by a host enzyme.
+- Dauer des kompletten Vermehrungszyklus des T4-Phagen? Ungefähr "25 Minuten".
+- Vorraussetzung dafür das der Lambda-Vorkopf mit DNA bepackt werden kann? Abbau des Nu3-Proteingerüsts.
+- Welcher Teil der Lambda-DNA kann ersetzt werden? J-N.
+- What are lambda "secondary attachment sites"? These are sequences where lambda can integrate, if the normal attB site on the chromosome is deleted. The frequency of integration at such secondary sites is very, very low, however so low that when wild-type attB site is present we will not witness integration at the secondary attachment sites.
+- The Lambda capsid protein requires help from which bacterial protein? Chaperonin GroE.
+- Der <one>Lambda-Repressor</one> besteht aus wievielen Domänen? Aus <one>2</one>.
+- Das Lambda Q-Protein bindet an welche DNA-Sequenz? An die <one>qut-Sequenz</one>.
+- At the ends of the lambda linear genome there are short single-stranded regions that are complementary, the so-called "cos sites". How long are these sites? "12 bp".
+- Das "Lambda cro-Protein" hat n Aminosäuren? "66".
+- For lambda integration, which two proteins are necessary? The "Intasome", which is a DNA-protein-complex consisting of phage protein Int and the bacterial protein IHF ("integration host factor").
+- Wir können Phagen in der Medizin aufgrund ihrer Wirtsspezifität zur Bestimmung von bakteriellen Erregern verwenden. Wie nennen wir dieses Verfahren? "Lysotypie".
+- Der "M13-Phage" infiziert E. coli Zellen über deren F-Pilus. Welche Domäne in welchem Protein ist hierbei wichtig? Die "N2-Domain" im "pIII Protein".
+- Nenne einen Effekt von M13 auf das infizierte Bakterium. A: Eine Infektion mit M13 verlangsamt das Wachstum des infizierten Bakteriums.
+- The lambda-phage expesses the Cro protein after it infects an E. coli cell. This protein then binds to OR3, which will prevent access to the "PRM promoter". This prevents expression of ... which gene? The "cI gene".
+- "Bacteriophage Lambda" can bind to an E. coli cell, by means of its ... protein in the tail tip. A: Its "J protein".
+- Name an advantage that "<u>phage therapy</u>" has over "antibiotic treatment" - at the least in regards to the application process itself. A: Phages can "infiltrate into biofilms" more easily than can antibiotics. This is also called "biofilm clearance".
+- When lambda is integrated into the E. coli genome as a prophage, what can we say about most of its genes? Most of its genes must be off; and have to be switched on, upon induction.
+- A bacteriophage must always overcome a cell wall for its propagation. Is this a true statement? No. "Mycoplasma" lack a cell well, yet do happen to have phages. URL: https://en.wikipedia.org/wiki/Mycoplasma
+- Welche Person gilt als "Begründer der Phagengenetik"? "Joshua Lederberg".
+- In the phage lambda, for "DNA replication", name two gene products that are required. A: (1) Gene product "O" (2) Gene product "P"
+- What are "Virophages" doing? They inhibit or impair the reproduction of the auxiliary virus (in the same infected cell).
+- What role does Lambda-Phage cII have? It protects cI against proteases - and "thus stabilizes it".
+- The "terminase" of the lambda phage first binds to the viral genome. It then proceeds to bind to which other structure? The "lambda terminase" will then bind to the "portal protein of an empty procapsid".
+- Transition between the "lytic lifecycle" and the "lysogenic state" involves ... ? "Site-specific recombination". URL: https://en.wikipedia.org/wiki/Site-specific_recombination
+- Who discovered "bacteriophages"? "Felix d'Herelle". URL: https://en.wikipedia.org/wiki/F%C3%A9lix_d%27Herelle
+- Nenne einen dsDNA-Phagen ausser Lambda und T4, aus einer Familie die mit "B" beginnt. A: Aus der Familie der "Bicaudaviruses", der "Sulfolobus virus STSV1".
+- Bacteria have anti-phage measures, called the Abi system, "abortive infection systems". Give another name for this system. A: "Phage exclusion".
+- Does the incorporation of the DNA into the lambda phage head require energy? Yes; it is "ATP dependent".
+- Besitzen Phagen Introns? Ja; der "T4"-Phage besitzt Introns, zumindest 3 (drei "self-splicing group I introns"), in Genen der "de-novo deoxyribonucleotide biosynthesis". URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1797299/
+- Phage lambda contains a gene, called "ral". What does this abbreviation stand for? "ral" stands for "restriction alleviation".
+- The lambda phage DNA integrates into the "BOB'" area in the bacterial genome. What is "O" here, aside from the name given to it aka the "core sequence"? O is "the crossOver point". ("O" may also be short for "Origin".)
+- Nenne zwei Beispiele für Regulationsstrategien in einer "Phagen-Kaskade". A: (1) "neuer Sigmafaktor" (2) "Antitermination"
+- "Fred Sanger" sequenzierte die Lambda-DNA. Diese Sequenz ist seit welchem Jahr bekannt? Sie dem Jahr "1982".
+- Phage T4 genome size? "38 kb" - it is "a fairly small T-phage".
+- Sometimes not all "dam sites" in phage DNA are methylated. Why may this be the case? Because phages may replicate so quickly that the "methylases" can not keep up with the newly generated DNA. A "heterogeneous restriction pattern" can occur with a sensitive enzyme.
+- The Lambda Phage J protein interacts with which E. coli molecule? With the "LamB porin".
+- In "phage display", why the name "display"? Because "the protein can be displayed on the surface of the phage".
+- Phagen wie "M13" (DNA-Phage) und "MS2" (RNA-Phage) haben zumindest eine prominente Gemeinsamkeit in ihrem Verhalten. Welche Gemeinsamkeit ist dies? Sie infizieren ausschließlich Bakterien mit "F-Pili".
+- What do we mean with "early infection of phages"? This is the period from entry of DNA into the bacterium, to the beginning of phage replication.
+- Name a "lambda phage protein" that can bind close to the "cos site". A: The "lambda terminase".
+- Definiere "virulenter Phage". A: Dies ist ein Phage der sich "ausschliesslich lytisch" vermehrt.
+- Was sind "Virophagen" + Beispiel angeben? Virophagen sind "Satelliten-Viren", die andere Viren infizieren. Der im Jahre 2008 entdeckte "Sputnik" ist ein Beispiel für einen Virophagen. URL: https://en.wikipedia.org/wiki/Virophage
+- What is meant with "phage therapy"? This is the application of bacteria-specific viruses, aka "phages", to combat uncontrolled and undesired bacteria such as those associated with "infectious disease".
+- A "prophage" can be induced to enter the lytic cycle by various "inducing agents". Other than UV radiation or petrochemical contaminants in the water, name a molecule that can cause this effect, starting with the letter "M". A: "Mitomycin C".
+- Give a specific example for a phage that makes use of "specialized transduction". A: The "lambda phage". URL: https://en.wikipedia.org/wiki/Lambda_phage
+- Der Kopfdurchmesser eines Lambda-Phagen beträgt, von-bis, etwa n nm? Etwa "50-60 nm".
+- What is the major characteristic feature of the "virulent phages"? When they replicate, they kill their host by lysing it.
+- Kann der Schwanzteil des Lambda-Phagen Virions kontraktieren? Nein.
+- Default outcome of a phage infection for a bacterium is, usually? The phage will kill (lyse) the bacterium.
+- Name two "generalized-transduction using phages". Where can these phages be found? A: (1)  "P1" (in "Escherichia coli") (2) "P22" (in "Salmonella typhimurium")
+- Give two examples for "Virophages". A: (1) "Sputnik Virophage" (2) "Organic Lake Virophage"
+- The "single subunit DNA-dependent RNA polymerase" from bacteriophage T3 is very closely related to which other, non-phage polymerase? It is very "closely related to mitochondrial RNA polymerases".
+- Which phage was used in the "Hershey-chase experiment"? The "T2-phage". URL: https://en.wikipedia.org/wiki/Hershey%E2%80%93Chase_experiment#Methods_and_results
+- Englisch für "Gerüstprotein" beim Phagenbau? "Assembly protein".
+- The "T7-Phage" has n genes? "25".
+- Benötigt der Lambda-Phage das Enzym "Polynukleotid-Ligase"? Ja.
+- For the phage lambda, what do we mean with "lytic products"? These include, for example, the "lambda head" or the "lambda tail components".
+- After injection of the lambda DNA, the phage DNA is covalently closed by ... ? The "host ligase".
+- The lambda phage genome has a sequence called "O", at "attB" and "attP". How is this sequence called? The "core sequence".
+- The "lambda cI repressor" mimics which other protein? "LexA"; this is also why the cI protein is "bound and cleaved by RecA".
+- Im Lambda-Phagen-Genom, nenne eine andere Bezeichnung für die "cos-Stelle". A: "m/m'".
+- Name a simple but effective way for a bacterial cell to protect itself against a phage without acting on the RNA/DNA of said phage at all. A: "Build a glycocalyx" around itself, which "acts as a protective structure".
+- Diameter of the Lambda-phage virion? About "65 nm".
+- Name two different "invasion types" for Bacteriophages into a cell. A: (1) "Injection" (for "tailed bacteriophages") (2) "Penetration" of the "entire virion" (proteins must protect nucleic acid)
+- The first mutations isolated and mapped in the phage lambda were ... ? Those that "changed the morphology of its plaques".
+- Name a "recombinase" that can be found in the "phage P1". A: The "Cre-recombinase". URL: https://en.wikipedia.org/wiki/Cre_recombinase
+- Im Lambda-Phagen, welcher "Promotor" ist für die Phagenkopf-Synthese wichtig? Der "PR'" Promotor. URL: https://www.ncbi.nlm.nih.gov/pubmed/1117996
+- What can we say about "secondary attachment sites" of phage lambda, aside from a much reduced frequency of integration? Secondary attachment sites resemble the authentic att sequence.
+- Who discovered "phage lambda"? "Esther Lederberg", in 1950.
+- Wo liegt der Origin des Lambda-Phagen? Im "O-Gen".
+- Phage T4 contains the unusual base hydroxymethylcytosine (HMC), instead of regular cytosine. Some bacteria have acquired modification-dependent systems that can exclusively cleave HMC-containing DNA, thus "preventing infection". How does Phage T4 counter this? Phage T4 acquired resistance to these enzymes through "glucosylation of HMC residues" ("glu-HMC").
+- Es gibt cI, cII und cIII im Lambda-Phagen. Wofür steht dieser Buchstabe "c" hier? "c" steht für "clear".
+- A phage may control transcription at initiation - name two different ways here. A: (1) synthesize a "new sigma factor" (2) synthesize a "new RNA polymerase"
+- Name the "most common way" for phages to "escape restriction". A: "Methylate the DNA".
+- What is the role of "Xis" in lambda-phage ingetration and excision? Xis is "required for excision"; it also "inhibits integration".
+- In the "phage lambda", the "tail fibers" are connected to ... ? The "basal plate".
+- In the lambda phage, the "immediate early" genes come right before the ... ? "Delayed early genes".
+- Die "red-Gene" von Lambda ... wieso diese Abkürzung? "red" steht hier für "reduction of recombination".
+- Name two important enzymes that are active shortly after phage DNA is injected. A: (1) host "ligase" (2) "topoisomerase" (for the supercoiling)
+- Lambda att-sites ... why was the name "att" chosen here? Att is short for "attachment".
+- Have Prophages been detected in "Archaea"? No.
+- Im Bakteriophagen Lambda, wie lang ist dessen attP Region? attP: "15 bp lang".
+- Structurally, phages fall into one of which three main groups? (1) "tailless" (2) "head with tail" (3) "filamentous"
+- The E. coli strain "K-12" carries a lysogenic lambda phage in its genome. When was this discovered? In "1950".
+- Die ssDNA-Phagen M13 und fd können nur F+ Bakterien, also "male bacteria", infizieren. Warum? A: Sie "müssen sich an den Pilus heften". (Weitere an den Pilus haftende Phagen sind RNA-Phagen wie f2 MS2 Qbeta, sowie noch DNA-Phage f1).
+- Nenne einen Phagen der "5-prime Hydroxymethylcytosin" statt Cytosin verwendet. A: Der Coliphage "T4".
+- Who was the original discoverer of bacteriophages? "Frederick William Twort".
+- How many bacteriophages exist on planet earth? 10 ** 31.
+- In the "lambda phage heads", how is the DNA kept? The DNA is present as a "linear double stranded DNA" ("dsDNA").
+- Durchmesser des "Sputnik Virophage", in nm? "50 nm".
+- Name a very interesting, external defence mechanism used by some bacteria against phages. A: These bacteria may sometimes "shed receptor material", as decoy; the phages bind to these receptors. This thus also constitutes a "resistance mechanism".
+- Name an unusual base that can be found in the "phage T4". A: The base "hydroxymethylcytosine" ("HMC").
+- What does the "Lambda cro gene" do when expressed? The "lambda cro gene" prevents synthesis of the "lambda repressor protein", by blocking transcription of the "cI-gene". (cro protein -> cI-gene) URL: https://en.wikipedia.org/wiki/Cro_repressor_family
+- Sometimes prophages can be induced "spontaneously" in a bacterial population. When does this usually happen? When bacterial cells enter the stationary phase.
+- "André Michel Lwoff" was the first to describe "lysogeny". In what year? In "1950".
+- Bacteria fight against phages via restriction enzymes. What can the phages do against this attack? They can "mutate their cleavage sites", via point mutations, so that the restriction enzymes no longer recognize the phage's genome.
+- 95% of all phages reported in the literature are members of which order? They belong to the order of "Caudovirales".
+- How do we call a phage that is integrated into the host chromosome? This is called a "prophage".
+- Which phages escape "restriction endonucleases" of bacteria in general? "RNA-based bacteriophages".
+- Name a phage that the E. coli strain K-12 genome carries. A: The K12 strain carries a "lysogenic lambda phage" in its genome.
+- Lambda-recombination occurs in ... ? In an "intasome". URL: https://en.wikipedia.org/wiki/Lambda_phage#Prophage_integration
+- Phages can create "holes" on the agar plate where bacteria may grow. How do we call these "holes"? "Plaques".
+- When was the Phage Lambda discovered? In the year "1950", by "Esther Lederberg".
+- Name an "anti-terminator protein" that phage lambda contains. A: "N". URL: https://en.wikipedia.org/wiki/Lambda_phage
+- Nenne ein Beispiel wie "Prophagen" in den lysogenen Zyklus übertreten mögen. A: Durch "UV Strahlung". URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC354795/
+- A. W. für "phage progeny"? "Lysate".
+- What is meant with the term "lysogenic conversion"? This is when prophages convert harmless bacterial strains into "pathogenic strains".
+- Der Bacteriophage MS2 hat wieviele Gene? "4". URL: https://en.wikipedia.org/wiki/Bacteriophage_MS2
+- A phage particle typically consists of a head. Give another name for this head. A: The "capsid".
+- Does the lambda phage, as "prophage", create new "att sites"? Yes - called "attL" and "attR".
+- Virophages will also infect "phycodna viruses". What global effect does this have? It "reduces algal death".
+- Warum benötigt der Lambda-Phage seine att-Stellen? Hier erfolgt die "Integration der Phagen-DNA in das bakterielle Genom".
+- In phage genetics what means a "chronic infection"? Also give an example for such a phage. A: Continuous release of progeny, such as in "M13-phages".
+- Why does the lambda genome have gene names such as N? Only a few phage genes were known in the early days, so a one letter code was initially used for phage genes.
+- The "Lambda-Phage" has cosN site where the DNA is nicked, but how long is the full cos sequence? It is about "~200 base pairs in length".
+- Ein Lambda-Phage setzt wieviele Nachkommen frei? Etwa 100.
+- Der "T4-Bacteriophage" hat n Gene? "150".
+- Nenne einen "dsDNA-Phagen". A: "Bakteriophage T4".
+- When the cI gene of the phage lambda is mutated, and no longer functions, can we recognize this in the E. colonies? Yes - "clear plaques will form", as there will be no lysogeny that could be established.
+- Wie verändert sich die optische Dichte einer bakteriellen Kultur wenn Phagen aktiv sind? Die Phagen lysieren die bakteriellen Zellen; dadurch "sinkt die optische Dichte".
+- "Bacteriophage Q" infects which target bacteria? "Bacillus megaterium". URL: https://en.wikipedia.org/wiki/Bacillus_megaterium
+- Do the "lambda cos-sites" base pair at room temperature? Yes.
+- Why the name "cI" for the lambda phage? cI stands for "clear plaques 1".
+- Wie lang ist der "Bakteriophage M13", in nm? "900 nm".
+- The "whisker" of phage T7 is attached to? The "connector".
+- For phages, what is the main task for the "antiholines"? The antiholin keeps the holin inactive, until the "time of lysis" occurs.
+- Do "lambda prophages" give the host cell a new property? Yes - since the lambda repressor is expressed in a lysogenic strain, such a strain is "immune to secondary infection by another lambda phage" (of the same immunity group).
+- In "lambda lysogenic pathway", how can we notice them by just looking at the plaque formed in E. coli? "Wildtype lysogens" will appear as "turbid plaque".
+- Wie "hoch" ist der Phage Lambda, in etwa, von "base plate" hin zur Spitze des "head"? Etwa "200 nm".
+- Why does the "lambda phage genome" require the N gene? The N gene is an antitermination factor that is required to "process the delayed early genes".
+- Does the lambda phage make use of "partially overlapped genes"? Yes.
+- Nenne two "phage characters"! A: (1) "Plaque Morphology" (2) "Host Range"
+- The "Cre recombinase" of the P1 phage recognizes? "loxP": a 34bp long sequence. URL: https://en.wikipedia.org/wiki/Cre-Lox_recombination
+- Someone may claim that "phage therapy" shows a "low inherent toxicity". What counter-argument may be given to this statement? Phages will "release bacterial components" when they lyse bacteria, which will release cell-wall containing compounds such as Endotoxin/LPS. (This is, however had, also the case when certain "cell-wall disrupting" antibiotics are employed.)
+- Gegeben sind x individuelle Bakterien. Wie viele Bakteriophagen existieren? 10 x.
+- Compare the "typical burst size" of phage T4 with picornavirus. A: (1) <one>T4</one>:           200 (2) <one>Picornavirus</one>: 100.000
+- Phage lambda may have the "red system". What does "red" stand for? "Recombination deficient".
+- What is the "receptor" for the "M13 Bacteriophages"? The "F-pilus".
+- Genom von M13? ssDNA.
+- The phenomenon of "phage restriction" on certain (bacterial) host strains led to the discovery of ... ? "Restriction enzymes" - aka "sequence-specific endonucleases".
+- The "phage X 174 protein J" codes for ... ? A "DNA condensation protein".
+- Nach einer erfolgten Lambda-Infektion einer bakteriellen Zelle kommt welches Enzym zum Einsatz? Die "Ligase".
+- Excision of the lambda phage requires which proteins? (1) "Int" (2) "Xis" (3) "IHF"
+- Can the "lambda tail" self-assemble? Yes. It will be subsequently attached to the phage head, after the DNA loading step.
+- Prophage genes "promoting host fitness" are called ...? Fitness factors.
+- Give one famous example for a "Virophage". A: The "Sputnik Virophage".
+- Wie lang ist das "P1 Phagengenom"? "115 kb".
+- Who coined the word "Bacteriophage"? "d-Herelle", in "1917".
+- How many percent of the prokaryotes in the ocean are infected by phages at any given time? At least 70%.
+- Wieso machen die kleinen Phagen grosse Plaques im Agar-Gel? Die kleinen Phagen können im Agar "besser diffundieren".
+- Warum der Name T4 oder T5 bei Phagen? T steht für "Type".
+- What is name of "the major bacteriophage group"? The order "Caudovirales": the "tailed bacteriophages".
+- In lambda phage, if the "lysogenic pathway is inactivated", the plaques of E. coli will ... look how? They will remain clear.
+- The lambda phage DNA will integrate into the BOB' area in the bacterial genome. What is B and B', respectively? (1) B  denotes the left  portion of the bacterial sequence into which lambda inserts. (2) B' denotes the right portion of the bacterial sequence into which lambda inserts.
+- The phage <one>PH42</one> attacks which bacterium? "Salmonella typhimurium".
+- Give an example for a phage that exists in "plasmid form in the cytoplasm". A: The "phage P1".
+- In 1915, the first bacteriophage was discovered. By which scientist? By "Frederick Twort".
+- Name an advantage that "phage therapy" may have, as a bactericidal agent, as opposed to an antibiotic. A: Bacteria that have been successfully infected by obligately lytic phages are unable to regain their viability. By contrast, certain antibiotics are bacteriostatic, such as tetracycline, and as a consequence may "more readily permit bacterial evolution towards resistance".
+- For phage lambda, what is the main criterium to fulfill the condition for packaging? That the two cos-sites are in the "correct distance range".
+- In general for some phages, when is the "lysogenic state" more frequently entered? If the "host is growing on an unfavorable carbon source".
+- In order to allow rolling circle replication, the lambda-phage has to produce a protein that inhibits "ExoV" of E. coli. Which gene product does so? The "gam gene" product (a historical designation; gam for "gamma protein").
+- What is the target receptor for "phage lambda"? It is a protein of the "maltose transport system", encoded by the lamB locus in the "malB operon".
+- What are <one>coliphages</one>? <one>Coliphages</one> are <two>phages that infect E. coli</two>. []
+- Hauptbaustein des Lambda Phagenkopf? Das "Gen E Protein".