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+# =========================================================================== #
+# === Transcription
+#
+# This file gathers knowledge about transcription, primarily in Eukarya but
+# perhaps also some entries for Prokarya. It also collects information
+# about transcription factors.
+# =========================================================================== #
+
+- Für die Initiation der Transkription von rRNA-Genen durch die <one>Pol I</one> ist welches Kontrollelement wichtig? <one>UCE</one> - <two>upstream control element</two>.
+- Verändert die Polymerase ihre Form während der Transkriptions-Elongation? Ja - sie wird <one>kompakter</one>.
+- <one>RNA polymerase II</one> (Pol II) transcribes RNA within a ... context. A: <one>chromatin</one> context.
+- The <one>carboxy-terminal domain</one> (CTD) of the alpha-subunit recognizes which element? The <one>UP-element</one>.
+- The <one>brachyury gene</one> <two>encodes a transcription factor</two>. <three>This has a lethal phenotype if inherited from ... which parent only</three>? From the <one>mother</one>. If it has been inherited from the father then it is not lethal.
+- What does the <one>sigma factor</one> allow the bacterial cell? The <one>sigma factor</one>, a bacterial transcription initiation factor, enables the specific binding of RNA polymerase (RNAP) to specific promoters.
+- The <one>aryl hydrocarbon receptor</one> <two>directly regulates the expression of ...</two> <three>which potent mitogen</three>? <one>Epiregulin</one>.
+- What happens to <one>RNA synthesis</one> in the presence of alpha-amanitin? <one>RNA synthesis</one> <two>slows down</two> from its normal rate of several thousand nucleotides per minute to just a few nucleotides per minute.
+- Provide <one>three examples</one> how <two>transcriptional arrests</two> <three>can be caused</three>. A: (1) <one>intrinsic DNA structures</one> (2) <one>DNA binding proteins</one> (3) drugs that bind DNA
+- Die <one>Proteinkinase A</one> <two>in Eukaryoten</two> <three>kann in den Zellkern wandern</three>. <four>Dort phosphoryliert diese Kinase dann welches Protein</four>? <one>CREB</one>: das <two>CRE-Bindeprotein</two>.
+- <one>CBP</one>, das <two>CREB-Bindeprotein</two>, ist <three>ein Koaktivator</three>, der darüberhinaus noch welche weitere Funktion besitzt? <one>CBP</one> agiert als <two>Histon-Acetyl-Transferase</two>.
+- Der Transkriptionsfaktor <one>SP1</one> trägt <two>drei Zinkfinger am ...</two> <three>Terminus</three>. A: Am <one>C-Terminus</one>.
+- Was genau liefert die <one>Transkription</one> in eukaryoten Zellen? Eine <one>prä-mRNA</one>.
+- <one>Transcription factors</one> and ... work together to initiate transcription. A: <one>coactivators</one>.
+- Give another name for <one>general transcription factors</one>. A: <one>Basal transcription factors</one>.
+- When regulatory proteins bind to promoter proximal elements, what effect will this have on transcription, in general? Transcription will be turned on.
+- In <two>eukaryotes</two>: which transcription factor remains bound to the polymerase during <one>transcriptional elongation</one>? <one>TFIIF</one>.
+- The <one>transcription cycle</one> of <two>Polymerase II transcription</two> <three>includes which five points</three>? (1) preinitiation (2) <one>initiation</one> (3) <one>promoter clearance</one> (4) <one>elongation</one> (5) <one>termination</one>
+- Das <one>Anheften des Poly-A Schwanzes</one> <two>an die 3'-OH Stelle einer mRNA</two> wird mitunter als <three>... bezeichnet</three>. A: <one>Tailing</one>.
+- <one>Bacterial transcription</one> <two>consists of which three general steps</two>? (1) initiation (2) <one>elongation</one> (3) <one>termination</one>
+- What does <one>positive control of transcription</one> mean? <two>Provide an example as well</two>. A: Here <one>transcription</one> <two>requires the binding of an activator protein to the DNA</two>. The Maltose-catabolism in <three>E. coli</three> is an example.
+- The <one>basal transcription apparatus</one> <two>in eukaryotes</two> consists of ... ? (1) <one>basal factors</one> (2) <one>RNA polymerase</one>
+- <one>Why</one> is <two>transcription in eukaryotes</two> <three>fairly slow</three>? This is <one>because proofreading steps are employed there during transcription</one>.
+- The <one>paired-box</one> transcription factor <two>Pax5</two> is a <three>master regulator</three> <four>of ... development</four>. A: <one>B-cell development</one>. URL: https://en.wikipedia.org/wiki/PAX5
+- <one>Jeder Transkriptionsfaktor</one> besteht generell aus <two>zumindest welchen zwei Domänen</two>? (1) einer <one>DNA bindenden Domäne</one> (2) einer <one>trans-aktivierenden Domäne</one>
+- <one>Transcription</one> <two>is coupled to splicing</two>. <three>What intracellular molecule may be indicative of this statement</three>? The <one>U2 snRNA</one>. This snRNA is required for RNA polymerase II pausing.
+- The <one>promoter</one> indicates ... and it also determines the ... ? A: The <one>promoter</one> indicates which of the two DNA strands is to read as the template. It also determines the transcription start site.
+- Can <one>electron microscopy</one> be used to demonstrate that RNA is transcribed from a DNA template? Yes - in 1970, Oscar Miller demonstrated that, by also employing deoxyribonuclease and Ribonuclease, on a Christmas tree representing a gene underoigng transcription.
+- Name an important task of the <one>CTD</one> that is <two>part of the RNA Polymerase II in eukaryotes</two>. A: The <one>CTD</one> <two>is involved in regulating transcription initiation</two>.
+- The <one>template for RNA synthesis is ... </one>? <one>Single-stranded DNA</one> (<two>ssDNA</two>).
+- In Eukaryoten wird der <one>Präinitiationskomplex</one> schrittweise gebildet, beginnend mit dem Transkriptionsfaktor <two>TFIID</two>. Dieser besteht aus <three>TBP</three> sowie <three>n TBP-assoziierten Faktoren</three> (den <four>TAFs</four>). <five>Wievielen TAFs genau</five>? <one>14</one>.
+- Are <one>the number of heptarepeats</one> <two>in the CTD of the RNA polymerase II</two>, in humans, important? <one>Yes</one>. <two>If we delete more than half of these repeats then this has a lethal consequence</two>.
+- <one>What effect</one> does the <two>6S RNA</two> have <three>in regards to transcription</three>? It <one>down-regulates</one> transcription from many <two>sigma-70 promoters</two>.
+- The <one>most common sequence element</one> found in the core promoter of eukaryotic genes is ... ? The <one>TATA box</one> (<two>TATAAA</two>).
+- For <one>pyrophosphorolytic editing</one>: which functionality of the RNA polymerase II is necessary? Its <one>3‘-5‘ exonuclease activity</one>.
+- Give another name for <one>initial transcription</one>. A: <one>Abortive Synthesis</one>.
+- Wer ist der <one>Transkriptionsaktivator</one> im <two>PhoB</two>/<two>PhoR</two> System? A: <one>PhoB</one>.
+- An den <one>EJC</one> bindet sich <two>NXF1</two>. <two>NXF1</two> <three>steht für ... </three>? <one>Nuclear RNA export factor</one>. URL: https://en.wikipedia.org/wiki/NXF1
+- <one>Warum</one> benötigt eine <two>mRNA</two> eine <three>Cap-Struktur</three>? Zum Einen als <one>Schutz vor Ribonucleasen</one>, zum anderen um die Translation einzuleiten.
+- If a transcription factor contains a <one>histone fold motif</one>, <two>what could we infer from this</two>? That <two>this transcription factor may be involved in the organisation of the chromatin structure</two>.
+- The <one>TATA box in eukaryotes</one> <two>typically begins at ... </two>? <one>-25 bp upstream</one> of the transcription start site.
+- Name <one>a reason</one> <two>why</two> <three>mRNA are folded</three>. A: <one>Folded mRNA</one> can render ribosome binding sites less accessible.
+- <one>IRES</one> in Eukaryoten <two>benötigen meistens Hilfsproteine</two>, die man <three>ITAFs</three> nennt. <four>Wofür steht diese Abkürzung</four>? <one>IRES trans-acting factors</one>.
+- Transcription of a topologically constrained DNA template causes ... ? <one>superhelical stress</one>.
+- <one>Which RNA polymerase</one> <two>contains a bipartite promoter</two>, that is, <three>a promoter consisting of two separate regions</three>? <one>RNA Polymerase I promoters</one>.
+- Name a <one>polymerase</one> associated with <one>transcriptional silencing</one>. A: The <one>Pol V</one>.
+- Nenne einen <one>key-step</one> in <two>transcription initiation</two> der <three>RNA Pol II</three>. A: <one>Phosphorylierung von CTD</one>.
+- In prokaryotes: <one>rho-independent terminators</one> <two>make up about n% of all terminators</two>? About <one>50%</one>.
+- The <one>core promoter</one> <two>can be found upstream of a gene</two>. It is the site to which ... binds. A: The <one>basal transcription apparatus</one>.
+- Wie nennen wir allgemein <one>die Proteine</one>, <two>die sich an Enhancer anlagern</two> und so die Transkription fördern können? <one>Transkriptionsaktivatoren</one>.
+- Name <one>five ways</one> <two>to assess the amount of transcripts in the tissue</two>. A: (1) <one>RNAseq</one> (2) Northern blot (3) semi-quantitative RT PCR (4) quantitative (real time) RT PCR (5) <one>microarrays</one>
+- <one>Wie</one> ist ein <two>Transkriptionsfaktor</two> definiert? Dies ist <one>ein Protein, das an definierte DNA-Sequenzen binden kann</one>.
+- Can we find <one>polycistronic mRNA</one> <two>in eukaryotes</two>? <one>Yes</one>, <two>although it is rare</two>. An example for an organism making use of polycistronic mRNA is <three>Caenorhabditis elegans</three>.
+- <one>When</one> is <two>the sigma factor</two> <three>released</three>? When the <one>RNA polymerase</one> <two>moves beyond the promoter</two>.
+- Kann die <one>Proteinkinase A</one> in Eukaryoten in den Zellkern wandern? <one>Ja</one>.
+- <one>Enhancers</one> <two>have all of the signatures of genes</two>, except ... ? Except that <one>they do not encode proteins</one>.
+- Give an example for a <one>Zinkfinger transcription factor</one> <two>that can only bind to RNA</two>. A: <one>TFIIIA</one>. This factor is required for transcription of the 5S rRNA genes. It has a higher affinity for 5S rRNA, as opposed to its affinity for binding to DNA.
+- Nenne <one>drei Typen</one> <two>cis-regulatorischer Sequenzen</two>, die die Transkription beeinflussen können. A: (1) <one>Promotoren</one> (2) <one>Silencer</one> (3) <one>Enhancer</one>
+- Name an interesting way <one>how the RNA polymerase may pause or slow down</one> <two>during the elongation phase during transcription</two>. A: <one>RNA secondary structures</one> may cause the RNA polymerase to slow down.
+- <one>Transcription</one> and <one>DNA-replication</one> are quite similar, but there is one fundamental, but trivial difference between these two processes. <two>Which one is that</two>? In <one>DNA replication</one>, all the nucleotides in the DNA molecule are copied, whereas in <two>transcription</two> only parts of the DNA molecule are transcribed into RNA.
+- The <one>first step in all transcription reactions</one> <two>is ... </two>? To <one>gain access to the DNA</one>.
+- <one>Wie</one> kann man experimentell nachweisen das <two>chromatin remodelling</two> stattfindet? Die Bereiche aktiver Transkription sind <one>gegenüber DNAse I sensitiver</one> als Heterochromatin-Bereiche, und genau dies nutzt man aus um nachzuweisen ob Chromatin da ist oder nicht. Ein Transkriptionsfaktor kann, logischerweise, nur dann binden wenn die DNA zugänglich ist.
+- Why is <one>backtracking</one> <two>important in transcription</two>? <one>Backtracking</one> is important for <two>transcriptional proofreading</two>, that is to reduce the number of errors made during transcription.
+- Die <one>Steroid-Transkriptionsfaktoren</one> besitzen <two>wieviele funktionellen Domänen</two>? <one>4</one>: A/B, C, <two>D</two>, E/F
+- Do <one>eukaryotic RNA polymerases</one> <two>contain a subunit that is related to the bacterial sigma factor</two>? <one>No</one>. The basal transcription factors substitute for this functionality instead.
+- In eukaryotes, <one>right before the elongation phase of transcription</one>, we can observe that many of the general transcription factors are left behind at the promoter. Does this have any useful purpose? <one>Yes</one>: that way they can serve to quickly reinitiate transcription with another RNA polymerase.
+- <one>Welche Terminationsarten der Transkription</one> sind in <two>E. coli</two> bekannt, und welche tritt häufiger auf? A: <one>Rho-abhängig</one> und <one>rho-unabhängig</one>. TODO: Add which ones ocurs more commonly.
+- If we observe <one>eRNA</one> (<two>enhancer RNA</two>), together with coactivators, promoting enhancer/promoter interaction: what can we furthermore assume to be the case? That <one>the DNA in-between will loop together</one>.
+- Bei <one>transcription coupled repair</one>: <two>welche Endonuclease fällt einem hierzu ein</two>? A: <one>UVR(A)BC</one>.
+- <one>Vault RNAs</one> (<two>vRNAs</two>) <three>are transcribed by ... </three>? <one>RNA polymerase III</one>.
+- Die <one>TBP</one> bindet an DNA, in einer Art Sattel. <two>Wieso verwendet man dieses Wort Sattel</two>? Da die <one>TBP</one> eine Art Plattform für weitere Faktoren ist und mit dieser Sattelform praktisch eine Plattform für andere Proteine bildet.
+- <one>How long does it take</one> to transcribe the <two>human dystrophin gene</two>? About <one>16 hours</one>.
+- <one>All</one> <two>transcription factors</two> <three>have which domain</three>, in general? A <one>DNA-binding domain</one>.
+- <one>Wie</one> kann <two>eine eukaryote Zelle</two> steuern, wie oft eine mRNA abgelesen wird? Über die Länge des <one>Poly-A-Schwanzes</one>. Bei der Translation wird der Poly-A Schwanz kontinuierlich verkürzt, aka <two>deadenyliert</two>.
+- A <one>transcription unit</one> <two>includes which three components</two>? (1) a <one>promoter</one> (2) an RNA-coding region (3) a <one>terminator</one>
+- Warum können wir den <one>Mediator</one> als <two>Schaltstelle</two> ansehen? Da er eine <one>Brücke</one> darstellt <two>zwischen der RNA-Polymerase II</two> und den verschiedenen Transkriptionsfaktoren.
+- In <one>eukaryotes</one>: <two>can RNA polymerase read the DNA sequence</two>? <one>No</one>, <two>due to chromatin</two> as well as a need to recognize cis-acting elements that have already bound to the DNA at hand.
+- <one>Benötigt</one> die <two>DNA-abhängige RNA-Polymerase</two> einen Primer? <one>Nein</one>.
+- <one>Welche Transkriptionsfaktoren</one> haben eine <two>SH2 Domäne</two>? A: <one>STATs</one>: <two>Signaltransduktoren und Aktivatoren der Transkription</two>.
+- Bei der DNA-Polymerase II binden <one>TFIIA</one> sowie <one>TFIIB</one> an <two>TFIID</two>. <two>Was ist deren unmittelbare Funktion</two>? Sie <one>stabilisieren TFIID</one>.
+- Provide <one>one example</one> for a <two>post-transcriptional control factor</two>. A: <one>miRNA molecules</one>.
+- The <one>largest class of transcription factors</one> <two>in animals</two> contains ... domains. A: <one>zinc-finger domains</one>.
+- The <one>CTD</one> of the RNA polymerase II can be phosphorylated on which aminoacids? (1) serine (2) <one>threonine</one>
+- <one>Welcher σ-Faktor</one> (Sigmafaktor) kodiert für die Synthese der Flagellen in E. coli? <one>σ²⁸</one>.
+- <one>How</one> could we experimentally determine regions in a given eukaryotic genome, that are <two>transcriptionally active</two>? We could employ the enzyme <one>DNase I</one>. URL: https://en.wikipedia.org/wiki/Deoxyribonuclease_I
+- In the human genome: are <one>transcription factors</one> more likely to bind downstream or upstream of the transcription start site? They are <one>about equally likely</one> to bind either upstream or downstream of the <two>transcription start site</two>.
+- Which <one>eukaryotic transcription factor</one> is <two>the most similar one to Sigma</two>? <one>TFIIF</one>.
+- <one>7SK</one> is <two>an abundant small nuclear RNA</two>. It plays a role in regulating transcription by controlling the positive transcription elongation factor of ... ? <one>P-TEFb</one>.
+- Was ist das <one>Transkriptom</one>? Dies ist <one>die Gesamtheit aller Transkripte</one>, also <two>mRNA</two>, in einer Zelle zu einem gegebenen Zeitpunkt. URL: https://en.wikipedia.org/wiki/Transcriptome
+- Name a <one>transcription factor</one> that is <two>activated</two> by the <three>TGF Beta-Family of proteins</three>. A: <one>SMADs</one>. URL: https://en.wikipedia.org/wiki/SMAD_(protein)#Role_in_TGF-%C3%9F_signalling_pathway
+- How do we call the complex of enzymes and proteins that perform transcription? The <one>transcription apparatus</one>.
+- <one>Can</one> one gene have two transcripts with opposite effects? <one>Yes</one>.
+- The <one>BRE element</one> <two>in eukaryotic RNA polymerase II promotoers</two> is also called ... ? <one>TFIIB recognition element</one>.
+- Do <one>bacterial cells</one> <two>possess pre-mRNA</two>? <one>No</one>.
+- Bessere Bezeichnung für den <one>Exon-Junction-Komplex</one>? <one>Exon-Exon-Junction-Komplex</one>. URL: https://en.wikipedia.org/wiki/Exon_junction_complex
+- Name <one>two different transcription factors</one> of the <two>AP-1 family</two>. A: (1) <one>fos</one> (2) <one>jun</one>
+- In eukaryotes: the <one>regulatory promoter</one> <two>can be found where</two>? Immediately upstream of the core promoter.
+- A <one>tRNA</one> <two>contains modified nucleotides</two>, such as <three>inosine</three> or <three>m...</three>? <one> Methylguanosine</one>. URL: https://en.wikipedia.org/wiki/Transfer_RNA
+- Wir sehen <one>regulatorische Elemente</one> wie <two>Enhancer</two> oder <two>Silencer</two>. <three>Wie</three> können diese zum Promoter positioniert sein? Entweder <one>proximal</one> oder <one>distal</one>.
+- <one>Can</one> <two>a generic promoter for eukaryotic cells</two> be described? <one>No</one>, as the promoter's descriptiopn depends on whether the promoter is recognized by RNA polymerase I, II or III.
+- What are the <one>transcription factors</one> of <two>tRNA genes</two>? <one>TFIII A</one>, <one>B</one> and <one>D</one>.
+- <one>RNA polymerase IV</one> is <two>found in plants</two>. <three>There it transcribes mostly ... </three>? <one>siRNAs</one>.
+- <one>Rel-Homologe</one> sind <two>Transkriptionsfaktoren</two> die in ihrer DNA-Bindungsdomäne welch anderen Proteinen ähneln? Der <one>NF-Kappa B Familie</one>.
+- Das <one>CBP-Protein</one> kann erst an CREB binden wenn … ? <one>Wenn Serin 133 phosphoryliert ist</one>. Tauscht man hingegen Serin 133 gegen ein Alanin aus, so wirkt CREB nicht mehr.
+- Die Transkription umfasst <one>die drei Phasen</one> <two>Initiation</two>, <two>Elongation</two> und <two>Termination</two>. <three>Welche davon wird am stärksten kontrolliert, von der Zelle</three>? Die <one>Initiation</one>.
+- In <one>bacterial transcription</one>: <two>rho-dependent terminators</two> are unusually rich in ... which nucleotide? In <one>cytosine</one> nucleotides.
+- What is the fate of the <one>sigma-factor</one> after it has bound to the promoter? It is usually released after initiation of transcription, although some RNA polymerases may retain the sigma factor throughout elongation.
+- <one>RNA Polymerase I</one> (<two>in eukaryotes</two>) transcribes what exactly? <one>18S</one>/<one>28S</one> <two>rRNA</two>.
+- Nenne <one>zwei Methoden</one>, mit derer Hilfe wir die Transkriptionsstartstelle eines Gens identifizieren können. A: (1) <one>S1-Nuclease-Methode</one> (2) <one>Primer-Extension-Methode</one>
+- The <one>enzymes</one> that ensure that each tRNA is coupled with the corect amino acid in an ATP-dependent process are called ... ? <one>Aminoacyl-tRNA synthetases</one>. URL: https://en.wikipedia.org/wiki/Aminoacyl_tRNA_synthetase
+- Give another term for <one>transcription attenuation</one>. A: <one>Premature termination of transcription</one>.
+- Wenn <one>ein Transkriptionsfaktor</one> aus <two>mindestens zwei Untereinheiten</two> besteht, was können wir vermuten das dieser Transkriptionsfaktor noch besitzen muss? Eine <one>Dimerisierungsdomäne</one>.
+- Wie kann man nachweisen das tRNAs auch ohne ungewöhnliche Basen ihrer zellulären Aufgabe nachgehen können? Durch <one>Deletionsexperimente</one> kann dies bewiesen werden. Jedoch nimmt dann die Genauigkeit der tRNAs ab wenn diese ungewöhnlichen Basen entfernt werden.
+- Which <one>eukaryotic polymerase</one> uses <two>a transcription</two> factor called <three>UBF</three>? The <one>RNA polymerase I</one>. URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC359177/
+- <one>How</one> is a <two>transcription unit</two> defined? This is a stretch of DNA that encodes an RNA molecule and the sequences necessary for its transcription.
+- The <one>transcriptome</one> can be mapped using ... arrays. A: <one>Tiling arrays</one>.
+- <one>Wieviele Transkriptionsfaktoren mit SH2 Domäne</one> sind im menschlichen Genom bekannt? Eigentlich nur die <one>STATs</one>.
+- Transcription of a topologically constrained DNA template causes ... ? <one>superhelical stress</one>.
+- Die Region von −200 bis zum Core-Promotor (bei Genen die von der RNA Polymerase II transkribiert werden) nennt man auch ... ? Dies ist der <one>proximale Promotor</one>.
+- Der <one>Core-Promotor</one> bei der <two>RNA-Polymerase II</two> inkludiert einen <three>Bereich von ... bis ...</three>, in etwa? Von <one>-35</one> bis <two>+25</two>.
+- Nenne eine andere Bezeichnung für <one>alternative splicing</one>. A: <one>Exon skipping</one>. URL: https://en.wikipedia.org/wiki/Exon_skipping
+- Ist für das <one>Funktionieren der Transkriptionsfaktoren</one> ein <two>Aufschmelzen der DNA</two> notwendig? Nein.
+- In der Genexpression, bei <one>E. coli</one>: wofür steht die Abkürzung beim <two>Transkriptionsfaktor FIS</two>? <one>Factor for inversion stimulation</one>.
+- Das <one>Anheften der korrekten 3'-CCA Struktur an eine reifende tRNA</one> wird durch ein <two>CCA-adding enzyme</two> katalysiert. Dieses gehört zur Superfamilie der ... ? <one>tRNA-Nucleotidyltransferasen</one>.
+- Nenne ein allgemeines Beispiel für <one>post-transkriptionelle Regulationsfaktoren</one>. A: <one>miRNA</one>. 
+- <one>Transcription factors</one> bind to ... ? A <one>sequence motif</one>.
+- Eine typische, <one>eukaryote mRNA</one> hat <two>nach dem Export aus dem Nukleus</two> in etwa n Adenin-Reste an ihrem 3' Ende? Etwa <one>200 Adenin-Reste</one> <two>am 3' Ende</two>. []
+- <one>tRNA transcription units</one> <two>contain promoter elements</two> that are <three>recognized by ... </three>? <one>RNA polymerase III</one> (<two>pol III</two>). []
+- Is the <one>promoter</one> - or rather, the sequence that builds a promoter - <two>transcribed</two>? <one>No</one>. []
+- The <one>TBP</one> (<two>TATA-binding protein</two>) binds to the minor or to the major groove of DNA? TBP binds the <one>minor groove of DNA</one>. []
+- The <one>human genome</one> <two>contains about n transcription factors</two>? About <one>1600</one>. []
+- Kann ein <one>Enhancer</one> in Eukaryoten auch <two>mehrere Gene beeinflussen</two>? <one>Ja</one>. []
+- <one>Which RNA polymerases in eukaryotes</one> <two>use a termination mechanism that is similar to rho-independent termination in bacteria</two>? <one>RNA polymerase III</one>. []
+- <one>Where inside of a given eukaryotic cell</one> can we typically find the <two>CBC</two> (<three>cap-binding complex</three>)? Within the <one>nucleus</one> of the cell. URL: https://en.wikipedia.org/wiki/Cap_binding_complex []
+- In Eukaryoten: <one>wo</one> in der Zelle werden die jeweiligen tRNAs mit einer Aminosäure beladen, also <two>"gecharged"</two>? Im <one>Cytoplasma</one>. URL: https://de.wikipedia.org/wiki/Cytoplasma []
+- Benötigt die <one>RNA-Polymerase I</one> eine <two>TATA Box</two>? <one>Nein</one>. URL: https://en.wikipedia.org/wiki/RNA_polymerase_I []
+- In Eukaryoten: <one>welche Untereinheit des Ribosoms</one> <two>bindet zuerst an die mRNA</two>? Die <one>40S-Untereinheit</one> des Ribosoms bindet zuerst an die mRNA. []
+- Are <one>coactivators</one> regarded as <two>transcription factors</two>? <one>Yes</one>. URL: https://en.wikipedia.org/wiki/Coactivator_(genetics) []
+- In general: <one>a modification via SUMO</one> <two>has what effect on a transcriptional regulator</two>? This will correlate with an <one>inhibition of transcription</one>. []
+- Der <one>Transkriptionsfaktor SP1</one> besitzt drei <two>"Zinkfinger"</two> ... <three>aber an welchem Terminus</three>? Am <one>C-Terminus</one>. URL: https://en.wikipedia.org/wiki/Transcription_factor_Sp1 []
+- <one>Which polymerase</one> <two>transcribes</two> the <three>snoRNAs</three>? The <one>RNA Polymerase II</one>. URL: https://en.wikipedia.org/wiki/Small_nucleolar_RNA []
+- The <one>sigma factor in bacteria</one> <two>is homologous to</two> <three>which eukaryotic factor</three>? <one>TFIIB</one>. []
+- Was passiert unmittelbar wenn <one>STAT-Transkriptionsfaktoren</one> <two>phosphoryliert</two> werden? Sie <one>dimerisieren</one>. URL: https://de.wikipedia.org/wiki/STAT-Proteine []
+- In <one>termination of transcription in eukaryotes</one>: <two>which of the three RNA polymerases require a termination factor</two> that is similar to the rho factor used in termainating the transcription of some bacterial genes? <one>RNA polymerase I</one>. []
+- During <one>transcription</one>, which DNA strand is being transcribed - the <two>template strand</two> or the <two>non-template strand</two>? The <one>temple-strand</one> <two>is the one that is transcribed</two>. []
+- <one>Termination of transcription in eukaryotes</one>, <two>by RNA polymerase II</two>, <three>requires which exonuclease</three> - <four>at the least in yeast cells</four>? The <one>Rat 1 exonuclease</one>. URL: https://en.wikipedia.org/wiki/Exonuclease#Discoveries_in_yeast []
+- <one>Which transcription factor</one> can <two>reprogram fibroblasts into muscle cells</two>? <one>MyoD</one>. URL: https://en.wikipedia.org/wiki/MyoD []
+- Die <one>CTDs</one> (carboxy-terminale Domäne) der verschiedenen RNA Polymerasen eukaryoter Spezies bestehen aus <two>Heptapeptidfolgen</two>. <three>Beim Menschen ist diese Sequenzfolge ... </three>? <one>YSPTSPS</one>. []
+- Das <one>CREB Protein</one>, <two>ein Transkriptionsfaktor</two>, besitzt die <three>P-Box</three>, die neben der Q1 und Q2 Box liegt. <four>Wieso der Name Q1 und Q2</four>? Da sie <one>glutaminreich</one> sind. []
+- In general: <one>transcription</one> <two>that takes place in the nucleus</two>, <three>occurs in ... </three>? <one>Transcription factories</one>. []
+- The most famous <one>C2H2 zinc finger protein</one> <two>in humans</two> is ... ? <one>Sp1</one>. []
+- Die <one>Proteinkinase A</one> <two>phosphoryliert welchen Transkriptionsfaktor im Zellkern</two>? <one>CREB</one>. URL: https://en.wikipedia.org/wiki/CREB []
+- Enthält <one>der Promoter in Eukaryoten</one> die <two>Transkriptionsstartstelle</two> (<three>TSS</three>)? <one>Ja</one>. []
+- In Eukaryoten: <one>wo</one> <two>werden die tRNAs synthetisiert</two>? Im <one>Nucleus</one>. []
+- Wenn ein Gen <one>hyperacetyliert</one> ist, können wir daraus etwas ableiten? <one>Ja</one> - und zwar das <two>dieses Gen vermutlich transkriptionell aktiv ist</two> oder dies sein könnte. []
+- Die <one>RNA-Polymerase</one> erstellt eine <two>transcription bubble</two>. <three>Wie lang ist das DNA-RNA Hybrid drin</three>? A: <one>8-9 Nukleotide</one>. []
+- <one>Which</one> of <two>the three RNA polymerases in eukaryotes</two> <three>transcribes most of the genome</three>? <one>RNA polymerase II</one>. It trancribes virutally the entire genome. []
+- Bei der <one>Polymerase II beim Menschen</one>: <two>welcher Transkriptionsfaktor</two> inkludiert <three>TBP</three>? <one>TFIID</one>. []
+- <two>tRNAs</two> besitzen fast immer ungewöhnliche Basen. Nenne eine dieser Base die mit dem Buchstaben <one>R</one> beginnt. A: <one>Ribothymidin</one>. URL: https://de.wikipedia.org/wiki/Ribothymidin []
+- <one>Which RNA polymerase</one> <two>synthesizes most of the hnRNA</two> (heterogeneous nuclear RNA)? <one>RNA Polymerase II</one>. []
+- <one>Verbleiben</one> <two>Introne</two> <three>im Zellkern</three>? <one>Ja</one>. []
+- <one>Wie</one> können <two>Eubakterien</two> mit ihrer RNA-Polymerase verschiedene Promotorklassen erkennen? Durch <one>Verwendung alternativer σ-Faktoren</one>. []
+- Can the <one>transcription factor</one> <two>CBP</two> <three>bind RNA</three>? <one>Yes</one>. []
+- Ungewöhnliche Basen findet man in bestimmten Bereichen in der tRNA. Die <one>D-loop</one> wird so genannt <two>aufgrund welcher Base</two>? <one>Dihydrouridin</one>. URL: https://de.wikipedia.org/wiki/Dihydrouridin []
+- In bacteria: a <one>rho-independent terminator</one> <two>contains an inverted repeat</two>, followed by a string of approximately six ... nucleotides. A: About <one>six adenine nucleotides</one>. []
+- <one>In eukaryotes</one>: do <two>enhancers</two> need to be near the promoter? <one>No</one>. []
+- <one>Promotoren</one> <two>für welche eukaryote RNA-Polymerase</two> <three>ähneln am meisten den bisher bekannten bakteriellen Promotoren</three>? Die <one>Promotoren</one> <two>der RNA-Polymerase II</two>. []
+- Do <one>methyl CpG groups</one> <two>directly block transcription</two>? <one>No</one>. []
+- <one>Pol I promoters</one> contain the <two>UCE</two>, <three>which is an abbreviation for ... </three>? <one>UCE</one>: <two>Upstream Control Element</two> []
+- Interagiert <one>TFIIH</one> im menschlichen Genom mit <two>regulatorischen Transkriptionsfaktoren</two>? <one>Ja</one>, wie zum Beispiel mit <two>p53</two> oder mit <two>E2F</two>. []
+- Can <one>Zinkfinger transcription factors</one> <two>bind to RNA</two>? <one>Yes</one>. []
+- <one>CTCF</one> <two>contains which metal</two>? <one>Zinc</one> - it is <two>a zink-finger protein</two>. []
+- The <one>U6 snRNA</one> <two>is transcribed by which enzyme</two>? By the <one>RNA Polymerase III</one>. []
+- Das <one>Inr-Element</one> (<two>Initiatorelement</two>) ist <three>purinreich</three> oder <three>pyrimidinreich</three>? Das <one>Inr-Element</one> ist <two>pyrimidinreich</two>. []
+- Das <one>Hefe-Genom</one> besitzt das <two>Gal-Regulon</two>. Dieses kontrolliert das Gal-Operon. <three>Welcher Faktor ist das zentrale Aktivatorprotein dieses Operons</three>? Der <one>Gal4-Transkriptionsfaktor</one>. <two>Dieser kann an upstream activing DNA Sequences von GAL binden</two>. URL: https://en.wikipedia.org/wiki/Gal4_transcription_factor []
+- Name <one>two general examples</one> for <two>distal DNA sequences</two> that can effect the efficiency of <three>transcription factors</three>. A: (1) <one>enhancers</one> (2) <one>silencers</one> []
+- Nenne einen <one>Transkriptionsfaktor in Eukaryoten</one>, der mit dem Buchstaben <two>M</two> beginnt. A: <one>Myc</one>. URL: https://en.wikipedia.org/wiki/Myc []
+- Is <one>transcription in archaea</one> <two>more similar to transcription in eukaryotes</two> than it is to <three>transcription in bacteria</three>? <one>Yes</one>. []
+- Das <one>Polyadenylierungssignal in Eukaryoten</one> ist ... ? <one>AAUAAA</one>. URL: https://flexikon.doccheck.com/de/Polyadenylierungssignal []
+- Der Transkriptionsfaktor <one>Myc</one> bindet zusammen mit seinem Dimer-Partner <two>Max</two> an ... ? Die <one>E-Box</one>.

data/lib/studium/exam_topics/translation_ribosomes_and_translational_control

@@ -0,0 +1,155 @@
+# =========================================================================== #
+# === Translation, Ribosomes and Translational Control
+#
+# Translation tag. Transcon tag. Und auch Transcon II tag.
+#
+# Auch Signaltransduktionsketten, sofern sich diese auf die Genetik
+# beziehen.
+# =========================================================================== #
+
+- Die <one>Effizienz der Translation</one> <two>einer gegebenen mRNA</two> hängt ... wovon in der Zell ab? Vom physiologischen Zustand der Zelle, also zum Beispiel dem Energiegehalt in der Zelle.
+- <one>Ribosome dissociation</one> <two>requires energy</two>? <one>Yes</one>, from <two>GTP hydrolysis</two>.
+- <one>Wie</one> beeinflussen Sekundärstrukturen einer RNA in der Nähe des 5'-Ende allgemein die Translation? Solche Sekundärstrukturen <one>reduzieren die Effizienz der Translation</one>.
+- What is meant with the <one>ribosome filter hypothesis</one>? That <one>ribosomes</one> <two>can selectively regulate the expression of specific mRNAs</two>.
+- Provide <one>two specific examples</one> for ribosomopathies. A: (1) <cadetblue>X-linked dyskeratosis congenita</cadetblue> (2) <one>Diamond Blackfan anemia</one>
+- <one>Transformed cells</one> <two>often contain which eIF in high number</two>? <one>eIF4E</one>.
+- Die <one>transformierende Wirkung von eIF4E</one> ist, zellulär betrachtet, worauf zurückzuführen? Wahrscheinlich aufgrund einer <one>selektiv besseren Translation</one> von "schwachen" mRNAs. Dies sind mRNAs mit einer stark strukturierten 5‘ UTR, wie zum Beispiel bei <one>myc</one>.
+- In presence of amino acids, <one>mTORC1</one> <two>is recruited to ...</two> through its interaction with the Ragulator:Rag complex. A: <one>Lysosomes</one>.
+- Why the name <one>trans-translation</one>? Because the ribosome <one>switches templates</one> during protein synthesis.
+- Wie können wir <one>experimentell</one> das Dissoziieren von Ribosomen bewirken? Durch <one>Herabsetzen der Mg2⁺ Konzentration</one>.
+- Wie könnten wir, experimentell, die <one>Translation unterdrücken</one>? Mit Hilfe der <one>RNA Interferenz</one> (<two>RNAi</two>).
+- <one>Welches Protein</one> <two>in Eukaryoten</two> interagiert mit <cadetblue>PABP</cadetblue> im Zuge der Translationsinitiation? <one>eIF4G</one>.
+- Was ändert sich wenn die <one>4E-BPs</one> <two>phosphoryliert vorliegen</two>? Sie verlieren den Kontakt zu eIF4E; dieses wiederum ist nun frei und <one>kann die Translation initiieren</one>.
+- The <one>loading of tRNAs</one> <two>is done by which enzymes</two>? By <one>Aminoacyl tRNA transferases</one>. URL: https://en.wikipedia.org/wiki/Aminoacyl_tRNA_synthetase
+- We have <one>mRNAs</one> that we call "TOP-RNAs". Why the name <one>TOP</one>? <one>5'</one> <cadetblue>terminal oligopyrimidine motifs</cadetblue>.
+- <one>Limitert</one> eine <two>eIF4E-Haploinsuffizienz</two> die Proteinsynthese? <one>Nein</one> - dies wurde auch experimentell bewiesen.
+- <one>Abundant proteins</one> means high rates of translation? <one>Not necessarily</one>. They may <two>be slowly translated</two> yet be very stable and thus produce high final concentrations.
+- What is <one>ribophagy</one>? <one>Ribophagy</one> is <two>a type of macroautophagy that selectively degrades ribosomes</two>.
+- Name <one>the two enzymes</one> that form the <two>Me7Gppp cap</two> <three>in eukaroytes</three>. A: (1) <one>guanylate transferase</one> (2) <one>guanine methyltransferase</one>
+- What are <one>ribosomopathies</one>? <one>Ribosomopathies</one> are diseases caused by alterations in the structure or function of ribosomal components.
+- What is the minimal distance between <one>polyribosomes</one>? They must be <one>80 nucleotides</one> apart.
+- In Eukaryoten erfolgt die Synthese cytoplasmatischer Proteine an nichtmembranassoziierten Ribosomen oder an membranassoziierten Ribosomen? An freien, das heißt an <one>nichtmembranassoziierten Ribosomen</one>.
+- Bei einigen Bakterien gibt es für welche zwei Aminosäuren keine eigenen Synthetasen? Für <one>Glutamin</one> und <one>Asparagin</one>. Hier werden die Aminoacyl-tRNA-Synthetase zuerst mit Glutaminsäure respektive mit Asparaginsäure beladen; ein zweites Enzym (eine Transamidase) wandelt dann die Säure in das gewünschte Amid um, eben in Glutamin oder in Asparagin.
+- Als Energieträger für die Translation fungiert ... ? <one>GTP</one>.
+- Das Prinzip der Translation lässt sich mit ... welchem Vorgang aus der Technik vergleichen? Mit dem <one>Morsen</one>.
+- Why is the ribosome's E site called that way? Because during translation, tRNAs will exit the ribosome again from the E site.
+- Like human childbirth, <one>the birth of a protein begins with ...</one>? <one>waiting</one>.
+- <one>Ribosome size</one> is measured in ... ? <one>Svedberg units</one>.
+- Some eukaryotic proteins contain signal sequences for transport into the lumen of the endoplasmic reticulum. How long, in n hydrophobic amino acids, are these signal sequences? Between 9 - 12 large hydrophobic amino acids.
+- Name <one>an antibiotic</one> with which we can modify <one>translational fidelity</one>. A: <one>Streptomycin</one>.
+- Was heißt <one>TransCon</one>? <one>Translational Control</one>. URL: https://en.wikipedia.org/wiki/Translational_regulation
+- <one>Wann</one> wurde <two>mTOR</two> (<three>Mammalian target of rapamycin</three>) entdeckt? Das Gen wurde im Jahre <one>1994</one> identifiziert. Die Aufgabe dieser Kinase ist es das Zellwachstum (und die Ribosomendichte) zu regulieren.
+- Was passiert wenn <one>4E-BPs</one> <two>phosphoryliert</two> werden? Sie verlieren ihren Kontakt zu eIF4E; dadurch kann die Translation eingeleitet werden.
+- Nenne einen <one>Inhibitor</one> der RNA-Helikase <two>eIF4A</two>. A: <one>Silvestrol</one>. URL: https://de.wikipedia.org/wiki/Silvestrol
+- Wenn <one>eIF4E</one> <two>dephosphoryliert wird</two>, welchen Effekt mag dies haben für die Zelle? Dies führt allgemein zu einer <one>Repression der Translation</one>.
+- <one>Which three factors</one> belong to the <one>eIF4F complex</one>? <one>AGE</one> (1) <cadetblue>eIF4A</cadetblue> (2) <cadetblue>eIF4G</cadetblue> (3) <cadetblue>eIF4E</cadetblue>
+- The protein <one>Maskin</one> plays an important role in translational control during ... ? <one>oocyte maturation</one>.
+- <one>eIF4E</one> ist oft <two>mit welcher Domäne assoziiert</two>? Mit einer <one>CERT-Domäne</one>.
+- The <one>CERT motif</one> contains in particular which nucleotide? <one>Cytosine</one>.
+- Kann das <one>Ribosom</one> <cadetblue>EJCs</cadetblue> auf einer mRNA entfernen? <one>Ja</one>.
+- <one>How</one> could a <one>translational repressor</one> activate genes? It could <one>repress a transcriptional activator</one>.
+- How was it shown that <one>eIF4E</one>, <two>the major cap-binding protein</two>, is NOT rate limiting translation in the mammalian genome? By making use of <one>an eIF4E haploinsufficient mouse</one>.
+- Wir sehen mitunter <one>zwei AUGs</one> <two>in einer Kozak-Sequenz</two>. Was ergibt sich hieraus? Die <slateblue>Proteine</slateblue>, die hierbei entstehen, unterscheiden sich oft an ihrem <one>N-Terminus</one>. (Meistens ist jedoch ein AUG das bevorzugte AUG; das andere wird seltener abgelesen.)
+- A polycistronic mRNA is useful in that we can regulate several genes/ORFs at the same time, but there is another interesting advantage for a polycistronic mRNA. Which one is that? The proteins that are synthesized here may be part of a multi-component protein, such as the ATPase or any other similar complex. Via close proximity, due to the polycistronic mRNA, the cell can ensure that assembly of this complex is simplified, by a coupled translation.
+- A <one>tRNA</one> has <two>how many major arms</two>? <one>Four</one> (<two>4</two>).
+- Welches Protein bindet in Eukaryoten an die <one>Cap-Struktur</one>, im Zuge der Translations-Initiation? <one>eIF4E</one>. URL: https://en.wikipedia.org/wiki/EIF4E
+- Wann ist der <one>Sigmafaktor 54</one> wichtig? Bei <one>N-Mangel</one> - also bei <two>Stickstoffmangel</two>.
+- Does <one>translation</one> occur in <two>stress granules</two>? <one>No</one>.
+- What is one of the most influencing factor as to whether the two ribosomal subunits, small and large, interact with one another? This depends on the presence of <one>Mg²++</one> - if the presence of Mg²++ is sufficiently high then the subunits will be together.
+- In Eukaryoten: der Vorgänger des <cadetblue>48S-Präinitiationskomplexes</cadetblue> ist ... ? Der <one>43S-Präinitiationskomplex</one>. URL: https://en.wikipedia.org/wiki/43S_preinitiation_complex
+- Name a major benefit of gene regulation, in regards to proteins, for any given cell. A: The encoded proteins will be produced only when they are required.
+- Why should we study <one>translational control</one>? To <one>cure</one>/<one>treat cancer</one>.
+- A ribosome has a large and a small subunit. How is the connection between these two units called? This is the <one>intersubunit bridge</one>.
+- Give an example for a <one>ribosomopathy</one>. A: The <one>Diamond-Blackfan anemia</one>.
+- Give another word or expression for <one>Initiation via IRES</one>. A: <one>Cap-independent translation initiation</one>.
+- Die <one>Translation</one> kann in vier Teilschritte unterteilt werden. Welche sind dies? (1) <one>Initiation</one> (2) <one>Elongation</one> (3) <one>Termination</one> (4) <one>Ribosome recycling</one>
+- Wieviele <one>binding sites</one> hat ein <two>Ribosome</two>? 3.
+- Wird TBP in Eukaryoten von der RNA Polymerase II benötigt? Ja.
+- How are ribosome and RNA-Polymerase kept in sync in E. coli? "NusE proteins" and "NusG proteins" (<one>E+G</one>) bind to the small subunit of the ribosome.
+- The protein <one>Maskin</one> can be found in which organism? <one>Xenopus</one>.
+- Was passiert wenn das ribosomela Protein S6 phosphoryliert wird? Dies fördert die Translation von mRNA.
+- TOR/mTOR ähnelt welcher Proteinkinase, zum Beispiel? <one>ATM</one>. URL: https://en.wikipedia.org/wiki/ATM_serine/threonine_kinase
+- Welches Protein hält eIF4E inaktiv? 4E-BP.
+- Kann mTOR 4E-BP direkt phosphorylieren? Ja.
+- Welchen Effekt erzielen die 4E-BPs, allgemein? Sie besetzen die Bindungsstellen an eIF4E; dadurch kann eIFE nicht mehr binden und somit kann keine Initiation der Translation stattfinden.
+- Enzymtyp von mTOR? <one>Proteinkinase</one>. URL: https://en.wikipedia.org/wiki/MTOR
+- Which person came up with the word "ribosome"? <cadetblue>Richard Roberts</cadetblue>, at the end of the 1950s. (Mnemonic: 3R, RRR, Richard Roberts Ribosome)
+- "Eukaryotic translation" initiation makes use of a "ternary complex". Which are its components? (1) <one>Met-tRNA</one> (2) <one>GTP</one> (3) <one>eIF2</one>
+- Nenne ein konkretes Beispiel wann der <one>nonsense-mediated mRNA decay</one> zum Einsatz kommt, im menschlichen Körpern beziehungsweise in Zellen des menschlichen Körpers. A:  Bei Immunzellen, im Zuge der zufälligen Rekombination von Genen für den T-Zell-Rezeptor oder für Antikörper.
+- What is the job of <one>eIF4A</one>? The job of this <one>ATPase</one> is to unwind secondary structure in the 5' untranslated region of a mRNA.
+- What is the fate of the <royalblue>eukaryotic initiation factors</royalblue> during translation? They <cadetblue>dissociate</cadetblue> from the ribosome <one>before</one> the elongation phase of translation begins.
+- Wann kommt es zu einer <cadetblue>Dephosphorylierung von eIF4E</cadetblue>? Bei einer <one>Mangelsituation</one>.
+- Nenne 5 posttranslatione Modifikationen! A: C"AMPUS". (1) Acetylierung (2) Glykosylierung (3) Methylierung (4) Phosphorylierung (5) Ribosylierung
+- Wann hat <one>Marilyn Kozak</one> die Kozak-Sequenz identifizieren? Im Jahre <one>1985</one>. URL: https://en.wikipedia.org/wiki/Marilyn_Kozak
+- Wofür steht die Abkürzung <cadetblue>4E-BP</cadetblue>? <one>eIF4E-binding protein</one>. URL: https://en.wikipedia.org/wiki/EIF4E
+- <one>CERT</one> is a special domain that may be associated with certain genes, in particular related to the activity of <one>eIF4E</one>. What does <one>CERT</one> stand for? <royalblue>Cytosine Enriched Regulator of Translation domain</royalblue>.
+- How was it shown that <cadetblue>eIF4E</cadetblue> can act as an oncogene? A knock down of eIF4E via antisense decreases the oncogenic and metastatic abilities of ras-transformed REFs (<one>rat embryo fibroblasts</one>).
+- On the molecular biology level, the term <one>ribosomopathies</one> is used to refer to diseases that may be caused by which two different targets/origins? (1) either by <cadetblue>a mutation in a rRNA gene</cadetblue> (2) or <cadetblue>a mutation in one of the ribosomal proteins</cadetblue>
+- Mammalian TOR complex 1 (mTORC1) and mTORC2 exert their actions by regulating other important kinases. Name two of these kinases. A: (1) the <gold>S6 kinase</gold> aka <one>S6K</one> (2) <one>Akt</one>
+- Nenne einen Weg für mTOR die Einleitung der Translation zu fördern. A: Über die <one>Phosphorylierung von 4E-BP</one>.
+- What do we mean with the <one>43S complex</one>? This is the small ribosomal subunit, the 40S subunit, and associated factors (such as eIF2/GTP/Met-tRNAi and eIF3).
+- Name a way how it could be demonstrated experimentally that the overexpression of eIF4E does not lead to the elevation of all proteins. A: We can incorporate <one>35S-Met</one> into proteins.
+- Gibt es <one>IRES-Initiation</one> innerhalb der Zelle? Ja, zum Beispiel beim <one>Myc-Protein</one>.
+- What makes ribosomes <one>specialized</one>? Different <crimson>isoforms</crimson> of ribosomal proteins.
+- The protein <one>Maskin</one> plays an important role in Xenopus, during the M-phase of oocyte maturation. What exactly is that role? This role is related to "microtubule assembly".
+- Eukaryotic genes may sometimes contain an <one>IRES</one>. Such genes are often involved where/how? These genes are often involved in the <lightskyblue>cellular stress response</lightskyblue>.
+- A single fully assembled ribosome covers how many nucleotides on a mRNA? <one>36</one>.
+- Gegeben ist die mRNA zu den eukaryoten Initiationsfaktoren eIF4A, eIF4G und eIF4E. Welche dieser mRNAs hat eine <one>IRES Sequenz</one>? Die <one>eIF4G mRNA</one>.
+- It was assumed that the major cap binding protein eukaryotic initiation factor, <cadetblue>eIF4E</cadetblue>, is the quantitatively limiting initiation factor for mRNA translation in eukaryotes. This was shown to be incorrect at a later time, but in which year, roughly, has this first been proposed? In ~1985 or 1987, respectively.
+- What is "ribosome shunting"? This is <cadetblue>a mechanism of translation initiation</cadetblue> in which ribosomes physically bypass, or <one>shunt over</one>, parts of the <royalblue>5-prime untranslated region</royalblue> in order to reach the initiation codon.
+- Nenne einen <one>eIF4-Faktor</one> der mit <one>PABP</one> interagiert. A: <cadetblue>eIF4G</cadetblue>. URL: https://en.wikipedia.org/wiki/EIF4G
+- Size of <one>eIF4E</one>, in kDa? <one>25 kDa</one>.
+- Haben <royalblue>weak mRNAs</royalblue> eher eine lange oder eine kurze <cadetblue>5'-UTR</cadetblue>? Eher eine lange 5'-UTR.
+- eIF4F consists of the three components eIF4G, eIF4E, and eIF4A. Which one of these three components binds to <one>eIF3</one>? <one>eIF4G</one>.
+- In der Genexpression, was heisst <one>RICTOR</one>? "rapamycin-insensitive companion of mTOR".
+- Which eukaryotic translation factor can be called <one>tumorigenic</one>? The <one>eIF4e cap-binding protein</one>.
+- When we apply <one>Puromycin</one> to eukaryotes, what happens? Puromycin causes <one>premature chain termination</one> during translation.
+- Wann ist <one>eIF4E</one> aktiv? Nur wenn es phosphoryliert vorliegt.
+- Does an overexpression of eIF4E lead to elevation of all proteins? No.
+- Members of the TACC protein family, such as Maskin, tend to localize to ... which object within the cell? To the centrosomes.
+- Give an example for a <cadetblue>DEAD-box helicase</cadetblue> that has a major role in eukaryotic translation. A: <one>eIF4A</one>
+- How do we call the first translation? <one>Pioneer round of translation</one> (removes EJCs) URL: https://www.cell.com/abstract/S0092-8674%2810%2900826-3
+- <one>eIF4E</one> can act as an oncogene, in particular by increasing the transformation-power of which other oncogene? <royalblue>v-myc</royalblue>. URL: http://cancerres.aacrjournals.org/content/69/19/7491
+- <cadetblue>Cytoplasmic polyadenylation</cadetblue> is one mechanism of controlling translation. It is driven by CPEB, which is a highly conserved, sequence-specific RNA-binding protein that binds to ...? CPEB binds to the "cytoplasmic polyadenylation element" (<one>CPE</one>).
+- Name a mechanism of controlling translation, in not more than two words. A: <one>Cytoplasmic polyadenylation</one>.
+- Does the eukaryotic ribosomal 40S subunit contain more different rRNA components than the 60S subunit does? <crimson>No</crimson>. The 40S subunit contains the 18S rRNA; the 60S subunit contains the 28S, 5.8S, and 5S rRNAs.
+- In eukaryotes, the addition of an extra <one>G</one> residue to the 5' part of a mRNA, via a 5'-5' bond, is done by which enzyme? The enzyme <one>guanylyl transferase</one>.
+- Das ribosomale Protein <one>S6</one> ist Teil welcher ribosomalen Untereinheit? Der <one>40S Untereinheit</one>. URL: https://en.wikipedia.org/wiki/Ribosomal_protein_s6
+- In Eukaryoten erfolgt die Erkennung eines falschen Stoppcodons während der Translation. Hierbei ist der "exon junction complex" - und welches Protein - wichtig? <one>UPF1</one>. URL: https://www.ncbi.nlm.nih.gov/pubmed/18066079
+- The <one>43S pre-initiation complex</one> in eukaryotes can scan in the <one>5' -> 3'</one> direction along the mRNA. It requires energy, from ... ? <one>ATP</one>.
+- In capping, the guanine used there is methylated at ... ? At <one>position 7</one>, at a <one>N atom</one>.
+- Nenne eine post-translationale Modifikation von <one>eIF4E</one>. A: <one>Phosphorylierung</one>.
+- Nenne eine <one>post-translationale Modifikation von eIF4E</one>. A: <cadetblue>Phosphorylierung</cadetblue>. eIF4E-P ist aktiv; es zu kommt zu einer vermehrten/effizienteren Proteinsynthese.
+- Andere Bezeichnung für "falsches Stoppcodon"? <cadetblue>PTC</cadetblue>: premature termination codon. URL: https://www.sciencedirect.com/science/article/pii/S0888754311001613
+- <one>Rapamycin</one> was isolated from ...? <one>Streptomyces hygroscopicus</one>. URL: https://en.wikipedia.org/wiki/Streptomyces_hygroscopicus
+- The <one>Kozak sequence</one> (10 nucleotides) goes like ... ? <one>GCCRCCAUGG</one>.
+- <one>Marilyn Kozak</one> has proposed a sequence; and also a hypothesis. How do we call her hypothesis? The <one>scanning hypothesis</one>. URL: https://en.wikipedia.org/wiki/Kozak_consensus_sequence
+- When we discover an <one>IRES</one> in a mRNA, what could we infer from this observation? Give at the least two assumptions that could be inferred from this. A: (1) This <cadetblue>could</cadetblue> be a <one>viral mRNA</one>. (2) The <cadetblue>mRNA</cadetblue> is, most likely, <one>uncapped</one>.
+- IRES-dependent translation in eukaryotic genes often promotes one of which two outcomes/effects? (1) it <one>can promote apoptosis</one> (2) it <one>can promote cell survival</one>
+- Name the three major components of a ribosome. A: (1) <one>ribosomal RNA</one>     (<one>rRNA</one>) (2) <one>ribosomal proteins</one>   (<one>RPs</one>) (3) <one>small nucleolar RNAs</one> (<one>snoRNAs</one>)
+- Give an example when <one>weak mRNAs</one> are, in particular, translated quite efficiently/often. A: When there is <one>an abundance of eIF4E</one>.
+- Give another word for "translational profiling". A: <cadetblue>Ribosome profiling</cadetblue>.
+- In eukaryotes, the enzyme <one>guanylyl transferase</one> will add an extra G residue to the 5' part of a mRNA. Which enzyme then adds a methyl group to this Guanine nucleotide? The enzyme <cadetblue>Guanine methyltransferase</cadetblue>.
+- For studying translation and gene expression, the <one>MEME Suite</one> is an important database. MEME stands for ... ? <one>Motif-based sequence analysis tool</one>. URL: http://meme-suite.org/
+- The <one>43S pre-initiation complex</one> is an important intermediate complex during cap-dependent translation initiation. It is recruited to the 5'-cap of eukaryotic mRNAs by which complex? By the <one>eIF4F complex</one>.
+- Does <one>capping</one> occur in prokaryotes? <one>No</one>.
+- If we apply <one>Wortmannin</one> onto some eukaryotic cells, what effect might this have? This will <one>increase ribosome concentration</one>.
+- In Eukarya: was muss die <deepskyblue>KOZAK-Sequenz</deepskyblue> auf jeden Falle enthalten? Ein <one>AUG-Startocodon</one>. URL: https://en.wikipedia.org/wiki/Kozak_consensus_sequence
+- Was heisst "mTOR"? <one>Mechanistic Target Of Rapamycin</one>. URL: https://de.wikipedia.org/wiki/MTOR
+- Seen from the ribosome, "wobbling" occurs where? At the "ribosomal A-site", where there is <cadetblue>an increased flexibility</cadetblue>.
+- Transkription über <steelskyblue>TBP</steelskyblue> bedingt eine TATA Box? Nein, nicht zwangsläufig. URL: https://en.wikipedia.org/wiki/TATA_box
+- Die <cornflowerblue>Trans-Translation</cornflowerblue> ist ein Reparaturvorgang. Welches Nukleinsäuremolekül steht in ihrem Mittelpunkt? Die <one>tmRNA</one>.
+- The important <one>CERT domain</one> can be found in which UTR of a gene typically? In the <one>5' UTR</one> of a gene.
+- Name three features that characterize a <one>weak mRNA</one>. A: (1) an inefficient cap-dependent translation (2) often containing IRES sequences (3) are often proto-oncogenes
+- Der <one>ternäre Komplex</one> bei der Initiation der Translation in Eukaryoten bestehen aus GTP, Initiator-tRNA und ... ? <one>eIF2</one>.
+- Kann die <one>5' UTR</one> einen <two>ORF</two> enthalten? <one>Ja</one>. []
+- Can <one>eukaryotic genes</one> contain an <two>IRES</two>? <one>Yes</one>. []
+- Ist <one>die Geschwindigkeit der Translation</one> <two>mit der Faltung von Proteinen gekoppelt</two>? <one>Ja</one>. []
+- The <one>energy source</one> <two>for peptide bond formation</two> <three>comes from ... </three>? <one>GTP</one>. []
+- Will <one>IRES</one> <two>still function if eIFs are downregulated</two>? <one>Yes</one>. []
+- What is meant with <one>uAUG</one>? This is <one>an upstream AUG</one>. []
+- The <one>ribosome</one> has <two>three special sites</two>, termed <three>E</three>, <three>P</three> and <three>A</three>. What do these letters stand for? (1) <one>E</one><two>xit</two> (2) <one>P</one><two>eptidyl</two> (3) <one>A</one><two>minoacyl</two> []
+- <one>Aminoacyl-tRNA-Synthetasen</one> <two>beladen tRNAs in wievielen Schritten mit der kognaten Aminosäure</two>? In <one>zwei Schritten</one>. []
+- Do all <one>tRNAs</one> <two>have the same sequence at their 3' end</two>? <one>Yes</one>: <two>CCA</two>. []
+- What is the <one>rate-limiting step</one> <two>in translation</two>? <one>Initiation</one>. []
+- What do we mean with the term "translation recoding"? Other nucleotide sequence information present in a mRNA can change the meaning of the genetic code at a particular site in the mRNA.

data/lib/studium/exam_topics/umweltbiotechnologie

@@ -0,0 +1,64 @@
+# =========================================================================== #
+# === UMWELTBIOTECHNOLOGIE
+#
+# Inkludiert auch Abwasser-Technologie, wie Flockung, und technische
+# Biotechnologie an der TU Wien, sowie den Abbau von Substanzen durch
+# Mikroorganismen, sofern dieser biotechnologisch genutzt werden kann.
+#
+# Auch Biotechnologie die sich mit Nachhaltigkeit auseinander setzt.
+#
+# "Abfallnutzung" ist hingegen in der Datei "abfall_als_ressource"
+# gesammelt.
+#
+# Umweltbiotechnologie.
+# =========================================================================== #
+
+- <one>Acidophilic bacteria</one>, such as Acidithiobacillus ferrooxidans, are increasingly being used to extract valuable metals, notably ... ? <one>Copper</one>.
+- <one>Hydrolases</one> are able to break down plastics. Give two specific examples for enzymes that are known to break down plastics. A: (1) <one>Cutinase</one> (2) <one>Lipase</one>
+- Microorganisms can produce enzymes that can cause degradation of plastic polymers. The enzymes that can do so belong to which family of enzymes? They belong to the <one>hydrolases</one>.
+- Why is plastic a problem, from the point of view of biotechnology? Plastic pollution has massively increased. As plastic is non-biodegradable it will accumulate in the environment and cause issues thereupon.
+- In den meisten Kläranlagen wird das Abwasser in n Stufen gereinigt? In <one>drei</one>.
+- Anderer Begriff für <one>kommunales Abwasser</one>? <one>Häusliches Abwasser</one>.
+- Is <one>cellulose</one> a form of stored glucose? <one>Yes</one>. URL: https://en.wikipedia.org/wiki/Cellulose
+- Welche <one>Kupferform</one> kann leicht ausgelaugt werden? <one>Kupfersulfat</one>, "CuSO4". URL: https://de.wikipedia.org/wiki/Kupfersulfat
+- In der (Umwelt)Biotechnologie: was ist der <one>CSB</one>? Chemischer Sauerstoffbedarf. Wird bestimmt durch Oxidation der Abwasserinhaltsstoffe durch "Kaliumdichromat". Der Wert erfasst den Sauerstoffbedarf zur Oxidation eines Großteils der organischen Stoffe. Sind im Abwasser auch oxidierbare anorganische Verbindungen, wie beispielsweise Sulfite, enthalten, werden diese ebenfalls als CSB erfasst. Für den CSB wird ein Wert von 120 g pro EW und Tag angesetzt.
+- Define the <one>Anammox-Process</one> in not more than two words. A: <one>Degrading Ammonium</one> (<two>NH4+</two>).
+- <one>Wann</one> wurde die Abwassertechnologie der Tropfkörper entwickelt? <one>1894</one>.
+- In der Abwasser-Technologie, was ist das <one>Phostrip-Verfahren</one>? Ein Verfahren um Phosphat aus Gewässern zu bringen. In einem Nebenstrom wird Polyphosphat durch Einstellung anaerober Bedingungen in Lösung gebracht.
+- <one>Which enzyme</one> starts the enzymatic biodegradation of cellulose? <one>Endo-glucanases</one>.
+- Um <one>Cellulose</one> zu degradieren werden verschiedene Enzyme benötigt. Unter anderem <one>EG</one> und <one>PMO</one>. Diese ABkürzungen stehen für? (1)  <one>EG</one>: Endoglucanase (2) <one>PMO</one>: Polysaccharide monooxygenases
+- Nenne ein Bakterium das "<ud>Ammonium</ud>" degradieren kann! A: "Candidatus Brocadia anammoxidans", ein anaerobes Bakterium.
+- Welche Faustregel gilt bei "halogenierten Verbindungen" und deren Abbau durch MO? Je mehr Halogenatome, umso langsamer der Abbau.
+- Was ist die "Wasseraktivität", und was sagt sie aus? Die Wasseraktivität ist ein Maß für "frei verfügbares Wasser in einem Material". Dieser Wert ist ein wichtiges Maß bezüglich der Haltbarkeit von Lebensmitteln.
+- Was geschieht unmittelbar wenn man "Abwässer in Flüsse" leitet? Der in Wasser gelöste Sauerstoffgehalt verringert sich.
+- Welches Bakterium ist für die "Anammox-Reaktion" verantwortlich? "Candidatus Brocadia anammoxidans".
+- Nenne einen Pilz der Phenole abbauen kann. A: "Trichosporum cutaneum".
+- Wofür genau steht die Abkürzung "Anammox"? ANaerobic AMMonium OXidation, oder auf Deutsch eben, "Anaerobe Ammonium-Oxidation". URL: https://de.wikipedia.org/wiki/Anammox
+- Der "chemische Sauerstoffbedarf" (CSB) wird bestimmt durch Oxidation der Abwasserinhaltsstoffe durch ... welche Substanz? "Kaliumdichromat".
+- Members of which (bacterial) genus are the predominant group of "soil microorganisms" that can "degrade xenobiotic compounds"? "Pseudomonas".
+- Name two different "*-phase bioremediation techniques". A: (1) "slurry-phase" bioremediation (2) "solid-phase" bioremediation
+- Definiere den Begriff <one>ex-situ Bioremediation</one>. A: Kontaminiertes Material wird vom Ort des Unfalles an einen anderen Ort gebracht und dann dort behandelt.
+- Wann tritt <one>Blähschlamm</one> öfters auf? Bei einem höherem Schlammalter.
+- Gib ein Beispiel an für "ex-situ Bioremediation"! A: slurry-phase Bioremediation.
+- Bei der Abwassertechnologie, was heisst das Kürzel "CSB"? Chemischer Sauerstoffbedarf.
+- Warum wird bei Bioremediation oft "Wasserstoffperoxid" eingesetzt? Weil dies in Wasser und Sauerstoff gespalten werden kann, und vor allem Sauerstoff für die Mikroorganismen verwendbar ist. Dies ist wichtig bei der Bioremediation.
+- Bei Bioremediation wird oft "Bioventing" eingesetzt. Was ist dies? Luft oder H2O2 in einen kontaminierten Boden pumpen.
+- Nenne 1 Bakterienart die häufig beim "Abbau von Xenobiotika" eingesetzt wird! A: Pseudomonas.
+- Welchen Zweck haben die "symbiotischen Schlammflocken" in den modernen Belebtsschlammverfahren? Sie sind Stützsubstanzen der Mikroben.
+- Warum wird Abwasser manchmal "Allylthioharnstoff" zugesetzt? Dieser Hemmstoff unterbindet die bakterielle Oxidation von Ammoniak (NH3), Ammonium (NH4+) und Nitrit (NO2-) zu Nitrat (NO3-).
+- Nenne ein klassisches Beispiel für eine "biotechnologische Abfallnutzung". A: Melasse.
+- Was ist die "Mischkanalisation"? Regen- und Schmutzwasser in einem Kanal.
+- Nenne vier Nachteile wenn man biotechnologische Verfahren verwenden möchte. A: (1) Sterile Bedingungen (2) Beseitigung der Bioabfallmasse (3) Qualitätsschwankungen biologischer Rohstoffe (4) biologische Systeme sind gelegentlich instabil
+- In der Biotechnologie, wovon sind die Abfallstoffe stark "abhängig"? Von dem jeweiligen Produktionsprozess.
+- Def. "Bioremediation"! A: Ist ein Prozess die Umwelt zu verbessern indem man lebende Organismen verwendet, die wiederum kontaminiertes Material degradieren können.
+- Gib eine andere Bezeichnung für den Begriff "Umweltbiotechnologe". A: "Biotechnologie der Umweltsanierung". 
+- Gib ein Beispiel für eine "anaerobe Abwasserreinigung". A: ANAMMOX.
+- Bei der Abwasserreinigung, im "Belebgungsbecken", welche Reinigungsstufen unterscheiden wir hier? (1) Mechanische Klärung (2) Biologische Klärung (3) Chemische Klärung
+- Der "BSB5-Wert" wird unter welchen Bedingungen gemessen? Unter <one>Standardbedingungen</one>.
+- Nenne 3 verschiedene biotechnologische Verfahren zur Abwasserreinigung. A: (1) Tropfkörper (2) Belebungsbecken (3) Turmbiologie
+- Was ist die "Ausfaulung"? Aus der aeroben Abwasserreinigung gebildeter Schlamm wird einer anaeroben Behandlung unterzogen.
+- In der Abwassertechnologie, gib zwei Beispiele für "Fremdwasser-Einstrom" an. A: (1) undichte Kanäle (2) Einleitungen von Drainagen
+- Nenne eine Hefe die in "mikrobiellen Abwassersensoren" verwendet werden. A: Arxula adeninivorans URL: https://de.wikipedia.org/wiki/Arxula_adeninivorans
+- Was ist der Zweck von Oxidationsbecken? Sie sollen dem (stehenden) Abwasser Sauerstoff zuführen.
+- Ein Rind produziert genau so viel Abwasser wie n Einwohner einer Stadt? 16.
+- Bei der Abwasserreinigung, welche 3 Stufen können unterschieden werden? (1) Mechanische Verfahren (2) Biologische Verfahren (3) Chemische Verfahren