studium 0.13.1

data/lib/studium/exam_topics/rna_and_dna

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+# =========================================================================== #
+# === RNA Tag. DNA TAG.
+#
+# Dies ist natürlich auch zum Teil Genetik, bezieht sich aber primär
+# auf die Nukleotide, nicht auf Vererbungsmuster und ähnlichem.
+#
+# Auch künstliche Nukleotide werden hier erwähnt und RNPs.
+#
+# miRNA, CRISPR, RNAi und siRNA werden jedoch in einer anderen Datei
+# gespeichert.
+# =========================================================================== #
+
+- <one>DNA</one> is the language of ... ? <one>Life</one>. []
+- We can distinguish between <one>strong mRNAs</one> and <one>weak mRNAs</one>. <two>Give a general example for a strong mRNA</two>. A: <one>House-keeping genes</one>.
+- Name all <one>four RNA secondary structures</one> that can be loops. A: (1) <one>Bulge</one>     loop (2) <one>Hairpin</one> loop (3) <one>Internal</one> loop (4) <one>Multibranch</one> loop
+- <one>Uric acid</one> is chemically related to ... ? A <one>purine</one>. URL: https://en.wikipedia.org/wiki/Purine
+- Do <one>histone mRNA</one> <two>have a poly(A) tail</two>? No - but they have a <one>HDE</one> (<two>histone downstream element</two>) at their 3-prime ends.
+- Welchen <one>Box(en)</one> hat die <two>tRNA</two> beziehungsweise die <two>5S RNA</two>? A: (1) <one>tRNA</one> besitzt <two>Box A</two> und <two>B</two>. (2) <one>5S RNA</one> nur <two>Box C</two>.
+- <one>RNA-binding proteins</one> tend to target what part of a RNA? Single-stranded regions within <one>secondary structure domains</one>, such as hairpin loops, internal loops or bulges.
+- Der Begriff <one>Riboswitch</one> wurde von <two>Ron Breaker</two> im welchen Jahr eingeführt? <one>2002</one>. URL: https://en.wikipedia.org/wiki/Riboswitch#History_and_discovery []
+- Nenne ein <one>DNA Nukleotid</one>, das <two>spontan desaminieren kann</two>. A: <one>Cytosin</one>; hin zu <two>Uracil</two> (<three>C→U</three>). []
+- Gibt es <one>RNA-Chaperone</one>? Ja – wie zum Beispiel <one>Hfq</one>. URL: https://en.wikipedia.org/wiki/Hfq_protein []
+- The <one>human genome</one> contains about <two>n different lncRNA</two> (long non-coding RNAs) genes, according to ENCODE 2012, roughly? (A good guess suffices to answer this question). A: <one>9649 lncRNA genes</one>, so almost 10.000.
+- Nenne ein Beispiel für einen <one>hochmolekularen, RNA-abbauenden Proteinkomplex</one>. A: Das <one>Degradosom</one>.
+- <one>RNA-binding proteins</one> (<two>RBPs</two>) exert many roles in the post-transcriptional regulation of gene expression in eukaryotic cells. Name one of the best-studied RBPs. A: <one>ZBP1</one>: <two>zipcode-binding protein 1</two>.
+- Die durchschnittliche molekulare Masse eines <one>dNTPs</one> beträgt <two>n Da</two>. A: <one>350 Da</one>.
+- The craziest <one>Drosophila gene</one> has been found to yield (max, approximately) n distinct mRNAs? <one>38.016 mRNAs</one>.
+- Die Bezeichnung <one>Introns</one> stammt von ... ? <one>Intragenic regions</one>. <two>Walter Gilbert</two> hat dieses Wort im Jahre 1978 geprägt. URL: https://en.wikipedia.org/wiki/Intron
+- Give <one>four examples</one> of modified RNA bases resembling Uridine. A: (1) <one>Pseudouridine</one> (2) <one>Ribothymidine</one> (3) <one>Dihydrouridine</one> (4) <one>Thiouridine</one>
+- Give another name for <one>guide RNAs</one>. A: <one>Small nucleolar RNAs</one>.
+- Bei <one>RNAi</one>: <two>wie werden Gene stillgelegt</two>? Mit Hilfe von dsRNA, die zur entsprechendenden mRNA komplementär ist.
+- Nenne <one>drei Punkte</one> wie der <two>DNA-Doppelstrang</two> stabilisiert wird. A: (1) durch <one>H-Brücken</one> (2) durch die <one>Basenstapelung</one> (3) durch <one>hydrophobe Wechselwirkungen</one>
+- What are <one>Aptazymes</one>? <one>Aptazymes</one> are <two>a class of engineered riboswitches</two>.
+- What does <one>hierarchical folding</one> mean in RNA biology? This means that the <one>secondary structure</one> forms first and then helices arrange to form "tertiary structure". This is the hierarchical part in folding.
+- There are three <one>Interacting Edges</one> <two>in a Hoogsten Base Pairing</two>. <three>How are these three called</three>? (1) <one>Watson-Crick Edge</one> (2) <one>Hoogsten Edge</one> (3) <one>Shallow-Groove Edge</one> []
+- Die <one>Z-Form der DNA</one> sieht man zum Beispiel bei welcher Nukleotidfolge? Bei <one> [CG]n</one> - also zum Beispiel bei <two>GCGCGCGCGC</two> (<three>[GC]₅</three>). []
+- What is <one>IVT</one> <two>mRNA</two>? This is <one>in vitro transcribed messenger RNA</one>. URL: https://stemcellsjournals.onlinelibrary.wiley.com/doi/10.1002/stem.2402 []
+- <one>Alternative splicing</one> <two>increases the genetic potential of a given genome</two>. Name another mechanism that increases the genetic potential. A: <one>RNA editing</one>.
+- Die <one>Identität einer tRNA</one> wird wodurch bestimmt? Über die <one>Anticodon-Loop der tRNA</one>. []
+- <one>Human genes</one> contain, on average, <two>how many exons</two>? A: <one>8-9 exons</one>. []
+- Warum können wir sagen das die <one>Purinbasen</one> wichtiger sind (für eine Zelle) als die <two>Pyrimidinbasen</two>? Die <one>Purinbasen</one> sind ATP und GTP. Beide sind nicht nur Bausteine von DNA und RNA, sondern übernehmen auch zusätzliche Aufgaben als <two>Signalmoleküle</two>.
+- <one>Who</one> were the two people who developed the <two>SELEX method</two>? (1) <one>Craig Tuerk</one> (2) <one>Larry Gold</one> []
+- <one>RNA</one> <two>forms biologically important structures</two>. Aside from tRNA or rRNA, name an interesting RNA 3D shape that forms an important structure. A: A <one>RNA thermosensor</one>.
+- Name a gene in the human genome containing introns that encode <two>multiple small nucleolar RNAs</two> (<one>snoRNAs</one>). A: The <one>human UHG gene</one>. URL: https://pubmed.ncbi.nlm.nih.gov/9387929/
+- Does the <one>TUTase enzyme</one> <two>add</two> to the 5' end or to the 3' end of a RNA? To the <one>3' end</one> only. []
+- <one>Q-Banden</one> werden durch welchen Farbstoff erzeugt? <one>Quinacrin</one>. URL: https://en.wikipedia.org/wiki/Quinacrine []
+- What are <one>tncRNAs</one>? <one>Tiny non-coding RNAs</one>. Actually, they are called <two>Transfer RNA-derived non-coding RNAs</two>. URL: https://pubmed.ncbi.nlm.nih.gov/34630945/ []
+- In a given average eukaryotic cell, the mRNA has n% of all total RNA in that cell? Approximately <one>3%</one> of the total RNA. []
+- Hat die <one>Zickzackform der Z-DNA</one> einen <two>geringeren Durchmesser</two> als die <three>B-Form</three>? Ja. []
+- <one>Antisense Oligonukleotide</one> werden oft <two>chemisch modifiziert</two>. <three>Welchem Zweck dient dies meistens</three>? Dies <one>erhöht die Stabilität des Stranges</one>.
+- <one>Wann</one> schlug <two>Walter Gilbert</two> die <three>RNA-Welt</three> Hypothese vor? <one>1986</one>.
+- <one>Why</one> is the <one>histone downstream element</one> (<two>HDE</two>) important? <one>Cleavage</one> occurs near this HD-Element.
+- In the cell, <one>Cytidine</one> can become <one>Uridine</one>. <two>This reaction is catalysed by which enzyme</two>? <one>CDAR</one>: <two>cytosine deaminase acting on RNA</two>.
+- <one>B-DNA</one> has <two>how many bp per turn</two>? <one>10.5</one>. URL: https://en.wikipedia.org/wiki/Nucleic_acid_double_helix#Helix_geometries []
+- <one>Wann</one> beobachtet man die <two>A-Form</two> der DNA? Wenn die DNA <one>dehydrated</one> ist - also <two>keine umgebenden Wassermoleküle vorliegen</two>. []
+- <one>piRNA</one> (piwi interacting RNA) hat welche Funktion? piRNA unterdrückt die Retrotransposition während der Spermatogenese.
+- What are <one>the substrates used in RNA synthesis</one>? <one>Ribonucleoside triphosphates</one>. []
+- A <one>RNA loop</one> is a region within a helix which is not base paired. <two>Which two major types of RNA loops can be distinguished</two>? (1) an <one>internal loop</one> (2) a <one>bulge</one>
+- What is meant <one>LSU RNA</one>? A <one>long subunit RNA</one>.
+- <one>DNA</one> kann durch <two>Formamid</two> denaturiert werden. Was sollte man (im Labor) noch verwenden, damit diese Denaturierung gut funktioniert? Man sollte dies <one>mit Wärme</one> kombinieren. 
+- The first sequence of a <one>transfer RNA</one> (<one>tRNA</one>) was published by Holley's team in which year? In <one>1965</one>.
+- <one>Splicing</one> occurs in eukaryotes - but how should we, more accurately and properly, call splicing really? <one>Cis-splicing</one>. []
+- Ob eine <one>RNA Sequenz</one> <two>IRES-Aktivität</two> hat oder nicht kann man wie herausfinden? Man kann ein <one>bicistronisches Reporter-Konstrukt</one> verwenden. []
+- Name the DNA nucleotides with a <one>NH₂ group</one>. A: <one>All</one> <two>but Thymidine</two>.
+- Bei der <one>SELEX Methode</one> werden Oligonukleotid-Stränge (<two>ssDNA</two> oder ssRNA) generiert. Wie werden diese derart generierten Oligonukleotid-Sequenzen genannt? <one>Aptamere</one>. URL: https://de.wikipedia.org/wiki/Aptamer []
+- Was ist schwächer: <one>A-U</one> oder <one>A-T</one>? A: A-U Basenpaarungen. Die sind überhaupt <one>am schwächsten</one>. []
+- What is <one>the best tetramer loop</one>? <one>T-C-C-T</one> - <two>pyrimidines are best here</two>. []
+- Wo wird, in Eukaryoten, <one>rRNA</one> transkribiert? Im <one>Nukleolus</one>. URL: https://de.wikipedia.org/wiki/Nucleolus []
+- <one>Splicing</one> (in human cells) involves how many different proteins? About <one>200</one>. []
+- In a <one>tRNA</one>, that last <three>CCA</three> at its 3' end: <three>which RNase cleaves off the 3' trailer</three>? The endonuclease <one>RNase E</one>. URL: https://en.wikipedia.org/wiki/Ribonuclease_E []
+- Nenne eine <one>chemische Gruppe die wir bei einem Purin</one> finden können, als Teil des Purins. A: Eine <one>Imidazol-Gruppe</one>.
+- Die <one>A-Form</one> der DNA hat <two>welche markante Besonderheit</two>? Die A-Form besitzt einen <one>offenen Raum im Inneren des Moleküls</one>.
+- Unterschiede zwischen <one>DNA</one> und <one>RNA</one>? (1) DNA ist <one>doppelsträngig</one>, RNA ist <one>einzelsträngig</one>. (2) <one>RNA</one> verwendet <one>Uracil</one> anstatt <two>Thymin</two>. (3) Desoxyribose hat eine OH Gruppe weniger als Ribose, und zwar fehlt die OH Gruppe an 2-prime Position.
+- How much percent of the human genome is <one>transcribed into RNA</one>? <one>~85%</one>. []
+- Nenne <one>zwei nicht-kodierende RNAs</one> die in der Translation eine besondere Rolle spielen. A: (1) die 23S rRNA, die die Peptidylbindung katalysiert (2) die <one>RNase P</one> die die Reifung von tRNA bewirkt, indem sie 5-prime Enden der tRNA erstellt
+- When <one>RNA</one> is hydrolyzed under <three>alkaline conditions</three>, what curious intermediate may form? A <one>2',3' cyclic monophosphate derivative</one>.
+- <one>RNA aptamers</one> can attach to their target molecule - but which two conditions have to be met for that to be successful? (1) They <one>require a specific shape</one>. (2) They <one>require the correct charge distribution</one>.
+- Name <one>two 3D structural elements of RNA</one>. A: (1) <one>ribose zipper</one> (2) <one>kissing loops</one>
+- Die 4 DNA Nukleotide in der DNA besitzen alle eine <one>-NH₂ Gruppe</one>, ausgenommen ...? <one>Thymin</one>.
+- The <one>Rho Protein</one> in E. coli, generally binds to ...? <one>RNA</one>. []
+- In a <one>LNA</one> (<three>locked nucleic acid</three>): which part of the molecule is locked? The <one>ribose moiety</one> of an LNA nucleotide has an extra bridge, connecting the <two>2' oxygen</two> and the <two>4' carbon</two>.
+- What is the <one>RNome</one>? All <one>cellular RNAs</one>. URL: https://link.springer.com/chapter/10.1007/978-981-13-1568-8_1 []
+- Mini-Mnemonic für <one>Purine</one> und <one>Pyrimidine</one> in der DNA bei der Paarung? <one>PuAG</one> und <one>PyCT</one>.
+- Räumlich betrachtet organisiert sich eine <one>tRNA</one> in etwa wie ... ? Wie eine Art <one>Kleeblatt</one> - hat also eine <one> Kleeblattform</one>, zumindest in 2D. In 3D besitzen tRNAs eine Art <two>L-Form</two>. []
+- Zwischen <one>A</one> und <one>T</one> bilden sich <two>zwei Wasserstoffbrücken</two>. Wo genau? (1) Zwischen <one>N1</one> von A und "N3" von T. Und ... (2) Zwischen "C4" von T und "C6" von A. (N1 / N3; C4 / C6, also 1 / 3, 4 / 6).
+- The first <one>RNA-pseudoknot</one> to be discovered was found in which genome? In the genome of the <one>turnip yellow mosaic virus</one>. URL: https://en.wikipedia.org/wiki/Turnip_yellow_mosaic_virus []
+- Name a post-translational modification of <one>ribonucleases</one>. A: <one>Phosphorylation</one>.
+- Liegt ein <one>RNA-Doppelstrang</one> immer in der <two>A-Form</two> vor? Ja. []
+- <one>Which enzyme</one> can add <two>nontemplated nucleotides</two>? The <two>Terminal deoxynucleotidyl transferase</two> aka <one>TdT</one>.
+- <one>DNA</one> illustrates the interplay between ... and ... ? A: <one>Form</one> and <one>Function</one>. []
+- Sterisch betrachtet: was ist besonders an der <one>A-Form der DNA</one>? Sie besitzt einen <one>offenen Raum</one> im Molekülinneren. []
+- <one>Welche DNA-Form</one> hat einen <cadetblue>offenen Raum im Molekülinneren</cadetblue>? Die <one>A-Form</one>. []
+- Wie können wir die <one>B-Form</one> der DNA in die <one>A-Form</one> überführen? Durch <one>Wasserentzug</one>. []
+- In welcher Form liegen <one>RNA-Doppelstränge</one> normalerweise vor? A: In der <one>A-Form</one>, da die 2 Strich-OH Gruppe keine B-Form zulässt (aufgrund <cadetblue>sterischer Beschränkungen</cadetblue>).
+- <one>Welche Form der DNA liegt</one>, bezogen auf die Ribose, als <three>Northern Pucker</three> vor? Die <one>A-Form</one>. []
+- Die <one>A-Form der DNA</one> entsteht bei drastischer Abnahme des Wassergehalts. Die Basenpaare sind nicht senkrecht, sondern gekippt. Um wieviel Grad? Um <one>70°</one>. []
+- Name <one>four group of genes</one> that can be transcribed by RNA Polymerase II. A: (1) <one>mRNAs</one> (of protein-coding genes) (2) <one>snRNAs</one> (3) <one>lncRNAs</one> (4) <one>microRNAs</one> []
+- To form a <one>Hoogsten Base Pair</one>, which Nucleotide must be <three>protonated</three>? <one>Cytosine</one>. URL: https://en.wikipedia.org/wiki/Hoogsteen_base_pair []
+- In <one>RNA</one>: which three base pairing possibilities exist within a long stretch of ssRNA? (1) <one>G-C</one> (2) <one>A-U</one> (3) <one>G-U</one> []
+- <one>HOTAIR</one> ist eine <two>ncRNA</two>. Die Abkürzung <one>HOTAIR</one> steht für ... ? <one>HOX transcript antisense RNA</one>.
+- Die Abkürzung <one>ncRNA</one> steht für ... ? <one>nicht-kodierende RNA</one> (eigentlich <two>non-coding RNA</two>). URL: https://en.wikipedia.org/wiki/Non-coding_RNA []
+- Nenne <one>die drei wichtigsten</one>/<one>gebräuchlichsten Veränderungen an einer eukaroyten mRNA</one>. A: (1) <one>Capping am 5' Ende</one> (2) <one>Polyadenylierung am 3' Ende</one> (3) <one>Entfernen der Introns</one>, durch <two>Splicing</two> []
+- In der <one>B-Form</one> der DNA liegt der Ribose-Zucker als ... Pucker vor. A: <one>Southern Pucker</one>. URL: https://en.wikipedia.org/wiki/Ribose#Structure []
+- Es gibt zwei grosse Familien an <one>snoRNPs</one>. Welche? (1) <one>C</one>/<one>D-Box</one> (2) <one>ACA-Box-snoRNP</one>
+- Give another name for <one>riboswitches</one>. A: <one>RNA-mediated regulation</one>.
+- What is the <one>ribose zipper</one>? The <one>ribose zipper</one> is a tertiary interaction formed by consecutive hydrogen-bonding between the backbone ribose 2prime-hydroxyls from two regions of the chain interacting in an anti-parallel manner.
+- Wieviele Stickstoffatome besitzen die <one>Purine</one>, die wir in DNA konkret finden können? <one>5</one> - zumindest <two>Adenin</two> URL: https://i.imgur.com/jEmIxBu.png []
+- Bei der <one>SELEX Methode</one> entstehen Aptamere. Was heisst <one>aptus</one>? <one>anpassen</one>. URL: https://en.wiktionary.org/wiki/aptus
+- <one>lncRNAs</one> besitzen per Definition mindestens n Nukleotide? Mindestens <one>200 Nukleotide</one>.
+- In der <one>DNA-Doppelhelix</one>: benachbarte Basen entlang der Helixachse sind <two>n nm</two> voneinander entfernt? <one>0,34 nm</one>. []
+- Why the name <one>Z-DNA</one>? Because in Z-DNA we can observe a <one>zigzag-arrangement</two> of the <two>backbone of the DNA molecule</two>.
+- The <one>RNase P RNA</one> consists of <three>two folded domains</three>. Which ones are these? (1) The <one>C-domain</one>: <two>Catalytic   domain</two> (2) The <one>S-domain</one>: <two>Specificity domain</two>
+- Can <one>inosine</one> pair, <two>via hydrogen bonds</two>, to <one>guanosine</one>? Yes. []
+- Name <one>three reasons</one> as to why eukaryotic mRNA is capped. A: (1) transport of mRNA from the nucleus to the cytoplasm requires a cap (2) protection of the mRNA from degradation via <two>exonucleases</two> (3) <one>initiation of translation</one>
+- Why does <one>stacking in the DNA-Helix</one> <two>increase stability</two>? Because <one>water molecules are excluded</one> that way between the base pairs.
+- Why is <one>DNA</one> <two>more resistant</two> to <three>base-catalyzed hydrolysis</three> than <one>RNA</one>? <one>DNA</one> lacks a <two>2'-OH group</two>. []
+- Name a molecule with a RNA component that shows a <one>concerted general acid-base catalysis</one>. A: <one>Ribonuclease A</one>.
+- Give another name for <one>all mRNAs in a human cell</one>. A: The <one>human transcriptome</one>. []
+- Can introns encode for <one>snoRNAs</one>? Yes, some do. []
+- <one>Genes containing introns</one> are also commonly called ... ? <one>Split genes</one>. []
+- A <one>nucleotide</one> has which two bonds? (1) an <one>ester bond</one> (2) a <one>beta-glycosidic bond</one>
+- Give two examples for <one>biological non-DNA moieties</one>. A: (1) <one>RNAs</one> (2) <one>proteins</one> []
+- Nenne ein allgemeines Beispiel für <one>eine RNA, die die Translation reguliert</one>. A: <one>Antisense-RNA</one>.
+- Sind <one>Transpositionen</one> in ein Intron ein Problem? Ja, möglicherweise - solche Transpositionen <one>können das Spleißen beeinflussen</one>. []
+- Name a RNA that is able to bind to <one>sigmafactor 70</one>. A: The E. coli <one>6S RNA</one>.
+- How many <one>major types of introns</one> are known? <one>4</one>. []
+- Wie wird aus einer <one>2'-deoxyribose</one> ein Nucleotide? Wir fügen eine Base hinzu, unter Entfernung von Wasser.
+- Wieso verwenden (manche) Mitochondrien <one>RNA Editing</one>? Die Genome sind stark kompromiert; durch die Verwendung von <one>A-editing</one> können <two>neue stop-codons erstellt werden</two>, zum Beispiel von TAG zu TAA, was UAA in der mRNA ergibt.
+- The <one>ADAR enzymes</one> have which charge? <one>ADAR enzymes</one> are <two>positively charged</two>. This is necessary because it will facilitate the interaction between the enzyme and the negatively charged dsRNA.
+- <one>Inosin</one> kann aus <two>Adenin</two> entstehen. Welches C-Atom von Adenin wird dabei desaminiert? Das <one>C6 Atom</one> von <two>Adenin</two>. []
+- <one>Why</one> may we use <two>two short hairpin RNAs</two> rather than merely one? Because of <one>off-target hits</one> that may be a target in another RNA.
+- Andere Bezeichnung für die rechtsdrehende Form der DNA und der linksdrehenden Form der DNA. A: (1) <one>rechtsdrehende Form</one>: <two>B-Form</two> (2) <one>linksdrehenden Form</one>: <two>Z-Form</two>
+- Which effect will we achieve by introducing <one>inverted repeats</one> into DNA? A <one>stem-loop</one> will form. []
+- <one>At which wavelength</one> do we measure <three>the optical density of DNA</three>? At a wavelength of <one>260 nm</one>. []
+- In <one>RNA Biology</one>: what does the abbreviation <two>RRM</two> stand for? <one>RNA recognition motif</one>. URL: https://en.wikipedia.org/wiki/RNA_recognition_motif []
+- Die <one>hydrolytische Desaminierung von 5-Methylcytosin</one> führt zu ... ? <one>Thymin</one>. URL: https://de.wikipedia.org/wiki/5-Methylcytosin []
+- The <one>TUTase enzyme</one> can add which nucleotide to RNA? <one>Uridines</one>. []
+- Give an example for a <one>RNA triplet base</one>. A: <one>U</one> ... <one>A</one> ... <one>A</one>. []
+- Die beiden Pyrimidine, <one>Thymidin</one> und <one>Cytosin</one>, haben in ihrer Base unterschiedlich viele N Atome. Wieviele? (1) <two>Thymidin</two> hat <one>2 N-Atome</one>. (2) <two>Cytosin</two>  hat <one>3 N-Atome</one>. []
+- Die ersten katalytischen RNAs, die mittels des <one>SELEX</one> in-Vitro-Evolutionsverfahren gewonnen wurden, waren ...? <one>RNA-Ligasen</one>. []
+- In <one>polyadenylation among eukaryotic cells</one>: is a cleavage signal retained in the mature mRNA? <two>Yes</two>, <one>the first AAUAAA cleavage signal is retained</one>, thus preceding the poly(A) tail.
+- Ein <one>Purin</one> hat wieviele N Atome im <three>Ringsystem</three>? <one>4</one>. []
+- <one>RNAi</one> is mediated by which complex? <one>RISC</one> - the <two>RNA Induced Silencing Complex</two>. URL: https://en.wikipedia.org/wiki/RNA-induced_silencing_complex []
+- Name a <two>motif</two> that is commonly found in many RNA-binding proteins (<cadetblue>RBPs</cadetblue>). A: The <one>RNA recognition motif</one> (<two>RRM</two>).
+- Name the two components of a <one>hairpin</one>. A: (1) the <one>hairpin stem</one> (2) the <one>hairpin loop</one>
+- We can identify at the least <one>two major problems with RNA as genetic material</one>. Name them. A: (1) <two>Large RNA-molecules are unstable</two>, so they <one>can not be a good storage medium</one>. (2) Because RNA is largely single-stranded, <one>no repair mechanism can work when RNA is mutated</one>.
+- In a <one>RNA aptamer</one>: give another name for the aptamer domain. A: The <one>ligand binding domain</one>. URL: https://en.wikipedia.org/wiki/Aptamer []
+- DNA up to n bp is rigid? <one>Up to 100 base pairs</one>. []
+- Gib ein konkretes Beispiel (<one>die Sequenz</one>), für ein DNA-Molekül, das eine <two>Z-Helix</two> ausbilden könnte. A: <one>GCGCGCGCGC</one> (<two>5x GC</two>). []
+- How does <one>Adenosine</one> have to be modified in order to yield <two>Inosine</two>? <two>Adenine</two> has to be <one>deaminated at carbon 6</one> (<one>C6</one>). []
+- Die <one>maximale Absorptionsrate</one>, in nm, von DNA und RNA liegt bei? <one>260 nm</one> (<one>A260</one>). Note that aromatic amino acids absorb light at 280 nm. []
+- Who discovered <one>catalytic RNA</one>? <one>Thomas Cech</one>. URL: https://en.wikipedia.org/wiki/Thomas_Cech []
+- <one>RNA editing</one> in trypanosomes takes place in a complex called ... ? The <one>editosome</one>. URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416509/ []
+- Nenne einen chemischen Unterschied zwischen <one>Adenin</one> und <one>Guanin</one>. A: <one>Guanin</one> hat eine <two>-C=O Gruppe</two>, <one>Adenin</one> hat <orange>keine</orange> -C=O Gruppe.
+- Do <one>RNA aptamers</one> have to fold up, in order to function properly? Yes. []
+- <one>Introns</one> were first discovered in which genome? In the genome of <one>adenovirus</one>. URL: https://en.wikipedia.org/wiki/Intron#Discovery_and_etymology []
+- What does the <one>purine riboswitch</one> sense exactly? <one>Cellular purine concentration</one>. URL: https://en.wikipedia.org/wiki/Purine_riboswitch []
+- What is <one>the essential precursor of DNA synthesis</one>? The <one>nucleotide</one>. []
+- Name two ways how we can, in the lab, <one>stop or prevent splicing</one>. A: (1) <one>omit ATP</one> (2) employ an antiserum that can block splicing
+- In the <one>snRNAs</one>, which U is missing? <one>U3</one>. []
+- Name the 3 enzymes employed during <one>RNA Capping</one>. A: (1) a "phosphatase" (2) a <one>guanyl transferase</one> (3) a <one>methyl transferase</one>
+- Die <one>glykosidische Bindung bei den Purinen</one> kann entweder in <three>syn-Konformation</three> oder in der <three>anti-Konformation</three> stattfinden. Pyrimidine sind stärker eingeschränkt - bei ihnen gibt es nur welche Konformation? Nur <one>anti</one>.
+- Where exactly can we find the <one>ribosomal peptidyl transferase activity</one>? In the <one>domain V</one> of the <two>23S rRNA</two> (<one>ribosomal RNA</one>). []
+- Wir finden in der <one>DNA</one> die Basen <three>Adenin</three>, <three>Guanin</three>, <three>Thymin</three>, Cytosin, Uracil. Wie heissen die korrespondierenden Nukleoside? A: (1) Adenosin (2) Guanosin (3) Thymidin (4) <one>Cytidin</one> (5) <one>Uridin</one>
+- <one>Cytidine</one> can be converted to <two>Uridine</two>. Cytidine has a -NH2 group, which, in Uridine, becomes ... ? A <one>-C=O group</one>. []
+- The <one>HOTAIR gene</one> contains <three>6.232 bp</three>. How long is the noncoding RNA molecule that it encodes? Only about <one>2.200 bp</one> in length.
+- Give one example for an <one>artificial ribozyme</one>. A: The <one>Diels-Alderase ribozyme</one>. []
+- Wann wurden die <one>Nucleinsäuren</one> entdeckt? <one>1869</one>. (Ein sehr <two>sexy year</two>) []
+- The <one>editosome</one> contains which three types of components? (1) gRNAs (2) the mRNAs to be edited (3) protein enzymes that will carry out the catalytic reactions on the mRNA
+- The enzyme <one>TUTase</one>, stands for ... ? <one>Terminal uridylyl transferase</one>.
+- In <one>RNA editing</one>: the <two>guide RNA</two> (<two>gRNA</two>) not only hybridizes to complementary sequences located on its mRNA substrate, but it also does what in addition to that? The gRNA recruits an endoribonuclease to the mRNA.
+- Welche intrinsische Eigenschaft ist für einen <one>riboswitch</one> extrem wichtig? Das dieser <one>ribsowitch</one> zumindest <two>zwei verschiedene Zustände</two> via <three>RNA-Sekundärstrukturen</three> besitzt.
+- If we compare <one>UV damage</one> against DNA and RNA, which one of these two is more resistant to UV damage? <cadetblue>RNA</cadetblue> is more resistant to <one>UV damage</one>. []
+- Welche <one>Sonderform des Spleißens</one> finden wir zum Beispiel in Chloroplasten? <one>Trans-splicing</one>. URL: https://en.wikipedia.org/wiki/Trans-splicing []
+- The abbreviation <one>crRNA</one> stands for ... ? <one>CRISPR RNA</one>. URL: https://en.wikipedia.org/wiki/CRISPR []
+- Is the eukaryotic 5' cap in any way connected with <one>introns</one>? Yes - <one>the presence of the cap influences the removal of introns</one>. []
+- What exactly means <one>negative strand RNA</one>? This refers to RNA that <one>is complementary to a mRNA</one>. []
+- <one>Durchmesser der DNA Helix</one>, in <cadetblue>n nm</cadetblue>? <one>2 nm</one>. []
+- Name <one>two types of regulation</one> that can happen on the level of the <two>mRNA</two>. A: (1) <one>transcriptional      regulation</one> (2) <one>post-transcriptional regulation</one> []
+- <one>In plants</one>: which RNA polymerases are involved in the synthesis of short non-coding RNAs? (1) <one>RNA polymerase IV</one> (2) <one>RNA polymerase V</one> []
+- Name a curious RNA structure that can form on a <one>circRNA</one>. A: The <one>microRNA sponge</one>.
+- Give another name for a <one>pre-mRNA</one>. A: <one>Primary transcript</one>.
+- Was bewirkt eine <one>antisense-RNA</one>? Eine Antisense-RNA bindet an die entsprechende mRNA und <one>verhindert deren Translation durch die Ribosomen</one>.
+- What task does the <one>aptamer domain</one> have, in a <three>riboswitch</three>? It <one>binds the metabolite</one>. []
+- In <one>RNA Thermometers</one>, who fulfills the metabolite functions? The <one>temperature</one>. []
+- In der Zelle: welche Polymerase transkribiert <cadetblue>lncRNAs</cadetblue>? <one>Polymerase II</one>. URL: https://en.wikipedia.org/wiki/Long_non-coding_RNA []
+- Bei der <one>de novo</one> Biosynthese der Pyrimidinnukleotide: welche Aminosäure liefert 3 C-Atome für den Pyrimidinring? <one>Aspartat</one>. []
+- What is a <one>scRNA</one>? <one>small cytoplasmic RNA</one>.
+- Was heisst <one>shRNA</one>? <one>Small hairpin RNA</one>; auch <one>short hairpin RNA</one> genannt. URL: https://en.wikipedia.org/wiki/Short_hairpin_RNA []
+- Which protein is <one>the catalytic engine of mammalian RNAi</one>? <one>Argonaute2</one> (<one>Ago2</one>). URL: https://en.wikipedia.org/wiki/Argonaute []
+- Was meinen wir mit einer <one>Heteroduplex</one>? Dies ist ein <one>DNA-RNA-Doppelstrang</one>. []
+- Vergleiche die <one>N-glykosidische Bindung</one> der <two>Purine</two> und <two>Pyrimidine</two> in bezug auf ihre <three>Säurestabilität</three>. A: (1) Die <two>N-glykosidische Bindung der Purine</two> ist <one>säurelabil</one>. (2) Die <two>N-glykosidische Bindung der Pyrimidine</two> ist hingegen ist <one>säurestabil</one>. []
+- Nenne ein konkretes Beispiel für eine RNA ohne freies Ende, ohne das es sich hierbei um ein Plasmid handeln würde. A: <one>Viroide</one>. URL: https://en.wikipedia.org/wiki/Viroid []
+- Die <three>snRNAs</three> (<one>U1U6</one>) in Eukarya haben eine Länge (in Nukleotide) von-bis ...? <one>110-220</one>. []
+- <one>Thymine</one> was first isolated from ...? <one>Thymus tissue</one>. URL: https://www.sciencedirect.com/topics/pharmacology-toxicology-and-pharmaceutical-science/thymine []
+- Give another term for <one>RNA bulge</one>. A: <one>Unpaired RNA</one>. URL: https://en.wikipedia.org/wiki/Internal_loop []
+- Which two states does the <one>tmRNA</one> have? (1) the <one>accomodated  state</one> (2) the <one>translocated state</one> []
+- In eukaryotes: does <one>polyadenylation</one> occur in the cytoplasm? Yes, in some cases this has been found to be true.
+- <one>Enol-BrdU</one> can base pair with ... ? <one>Guanin</one>. []
+- <one>Friedrich Miescher</one> entdeckte im welchen Jahre <two>DNA</two>? <one>1869</one>. (Mnemonic: <two>sexy 69</two>). []
+- Die <one>B-DNA Form</one> sieht man wann? Wenn <one>Wasser</one> vorhanden ist. []
+- How to find out which part of an <one>RNA enzyme</one> is important? We can perform <one>substitution experiments</one>. []
+- Give another term for <one>an extremely young pre-mRNA</one>. A: A <one>nascent pre-mRNA</one>.
+- Der <one>Pyrimidin-Ring</one> wird, biochemisch betrachtet, neu synthetisiert. Ausgehend von Hydrogencarbonat, NH3 und 2x ATP, welche Substanz kommt danach, das ein N und ein C-Atom für den Pyrimidin-Ring liefert? <one>Carbamoylphosphat</one>. []
+- Wie lange sind die <one>CRISPR-spacers</one> (von - bis)? <one>20-72</one> base pairs.
+- Which person gave <one>Introns</one> their name? <one>Walter Gilbert</one>. URL: https://en.wikipedia.org/wiki/Walter_Gilbert []
+- Die <one>ADAR Familie</one> konvertiert welches Nukleotid zu ... ? <one>A → I</one> (<two>Adenosine → Inosine</two>).
+- Welche <one>zwei Stoffwechselwege</one> gibt es um <three>Nukleotide</three> zu synthetisieren? (1) <one>de-novo Synthese</one> (2) <one>salvage pathway</one> []
+- Name the two main characteristics that influence the melting temperature of DNA. A: (1) <one>G-C content of DNA</one> (2) <one>ionic strength of the solution</one> []
+- Why the name <one>RNA Editing</one>? Because the <one>nucleotide sequence of a mRNA</one> is altered.
+- Can <cadetblue>RNA editing enzymes</cadetblue> also affect DNA molecules? Yes. []
+- Do <one>RNA Plasmids</one> exist? Yes. []
+- The very important <one>23S rRNA</one> has how many nucleotides? <one>2904 nucleotides</one> - at the least in <two>E. coli</two>. []
+- <one>RNA aptamers</one> are in some ways similar to which other biological molecule? To <one>protein antibodies</one>. []
+- Die <one>pRNA</one> ist assoziiert mit welchem Pol-Promotor: <two>Pol I</two>, <two>Pol II</two> oder <two>Pol III</two>? Mit dem <one>Pol I Promotor</one>. URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3929421/ []
+- Give one example where we might find the <one>tetraloop-tetraloop receptor motiv</one>. A: In the <one>azoarcus-intron</one>.
+- What is the most important <one>effect of mRNA polyadenylation</one>? This <two>increases</two> <one>the stability of the mRNA</one> at hand. []
+- <one>Divalent metalions</one> are required for which <three>cellular activity</three>, without participation of a Polymerase? <two>Splicing</two> of <one>group I introns</one>. []
+- What does the name <one>piRNA</one> stand for, in genetics? <one>Piwi-interacting RNA</one>. URL: https://en.wikipedia.org/wiki/Piwi-interacting_RNA []
+- Der <one>Elektronendonator</one> für die Reduktion von Ribonucleotiden zu Desoxyribonucleotiden ist ... ? <one>NADPH</one>. URL: https://de.wikipedia.org/wiki/NADPH []
+- The <one>hammerhead self-cleaving sequence</one> has <three>n stems</three>? <one>3</one>. []
+- Pohl und Jovin haben im Jahre 1972 die <one>Z-Form der DNA</one> entdeckt. Welche Technik haben sie dabei eingesetzt? <one>CD-Spektroskopie</one>. []
+- A demonstrated role for <one>circRNAs</one> is to act as a ... sponge. A: <one>microRNA sponge</one>. []
+- How many different enzymes are needed for the <one>RNA capping</one> step? <one>3</one>. []
+- A <one>messenger RNA</one> contains which three primary regions? (1) <one>5' untranslated region</one> (2) a <one>protein-coding region</one> (3) a <one>3' untranslated region</one> []
+- Are <one>UTRs</one> part of the exons? <one>Yes</one> - <two>they remain in a mRNA after all</two>. []
+- Durch <one>aggressive Sauerstoffverbindungen</one> kann welche Veränderung in der DNA entstehen? Eine <one>8-oxo-Guaninbase</one>. []
+- <three>Extracellular vesicles</three> may contain <one>TERRA</one>. What is <one>TERRA</one>? <two>TERRA</two> refers to <one>telomeric repeat-containing RNA</one>.
+- Can <one>dyad symmetry</one> also occur in RNA? No - at the least <one>not in ssRNA</one>. []
+- We can say, for any given <one>mRNA</one>, that there is <two>a path</two> from <three>"the cradle to the grave"</three>. What is meant with cradle and grave here, in this respect? (1) <one>cradle</one>: <two>transcription of this mRNA</two> (2) <one>grave</one>:  <two>mRNA decay of this mRNA</two>
+- The <one>pKa</one> of the phosphate backbone in DNA and RNA lies where? Near <one>0</one>. []
+- Wo in der mRNA finden wir das <one>SECIS Element</one>? In der <two>3-prime untranslated region</two> (<one>3'-UTR</one>). []
+- Die <one>DNA-Doppelhelix</one> hat was für eine <three>Drehrichtung</three>? Die <two>DNA-Doppelhelix</two> ist <one>rechtsgewunden</one>. []
+- Give an example for <one>a Ribozyme</one> that <three>acts on a carbon center</three>. A: The <one>peptidyl transferase</one> in the <two>ribosome</two>. []
+- In <one>RNA-Editing</one>: which nucleotide is the most likely one to be added? <one>Uridine</one>. URL: https://en.wikipedia.org/wiki/Uridine []
+- Can <one>RNA-binding proteins</one> bind to both ssRNA and dsRNA? Yes - at the least we know of such proteins that can bind ssRNA or dsRNA. []
+- In <one>RNA base pairing</one>: which of the three pairs <three>G-C</three>, <three>A-U</three> and <three>G-U</three> is the least stable one? The <one>G-U base pair</one>. []
+- The <one>messenger RNA</one> (<two>mRNA</two>) functions as the template for ...? <one>Protein synthesis</one>. []
+- Was heisst <one>RNAi</one>? <one>RNA Interferenz</one>. []
+- The <one>RNA recognition motif</one> (<two>RRM</two>) is present in up to <three>n% of all proteins</three>. A: About <one>1%</one> of all proteins. []
+- Wie unterscheidet sich <one>Uracil</one> von <one>Thymin</one>? A: <two>Uracil</two> hat keine -CH3 Gruppe. Yap - <one>überhaupt keine einzige Methylgruppe</one>. []
+- Was meinen wir mit der <one>scaffold-Funktion</one> der RNA? RNA kann als Gerüst zur Anlagerung von Proteinfaktoren dienen; so entstehen zum Beispiel große RNPs.
+- Wo in einem Molekül sind <one>Wasserstoffbrücken in der DNA</one> allgemein möglich? Zwischen <one>N-N</one> und <one>N-O</one>. []
+- Give another expression for the <one>GU-AG motif</one>. A: <one>Splice here!</one> []
+- Welche Person prägte den Begriff <one>RNA-Welt</one>? <one>Carl Woese</one>. URL: https://en.wikipedia.org/wiki/RNA_world []
+- <one>Deamination of guanine</one> results in the formation of ... ? <one>Xanthine</one>. URL: https://en.wikipedia.org/wiki/Xanthine []
+- How are <one>two nucleotides coupled to one another in dsDNA</one>? Via <one>phosphodiester linkage</one>. []
+- May <one>tRNA genes</one> contain introns? Yes; either <one>zero or one</one> (<cadetblue>one or none</cadetblue>). []
+- Nenne die drei charakteristischen Gruppen bei <one>Thymin</one>. A: (1) <one>-CH3</one> (2) <one>-C=O</one> (3) <one>-C=O</one> []
+- Which <one>three base pairs</one> can be found in <three>RNA</three>? (1) <one>A-U</one> (2) <one>G-C</one> (3) <one>G-U</one> []
+- Es gibt <one>Gewebe-spezifisches RNA-Editing</one>, ausgehend von <two>C</two> (Cytidin) hin zu ... ? <two>C → U</two>, also hin zu <one>Uridin</one>. []
+- Wie können wir <one>kleine RNAs</one> suchen und finden? <three>Knockout der RNA Sequenz</three>; danach Durchführen einer <one>globalen Transkriptomanalyse</one>.
+- Name the <one>three general elements</one> of a nucleotide. A: (1) <one>Phosphate</one> (2) <one>Pentose</one> (3) <one>Base</one>
+- The <one>enol form</one> of <three>Cytosine</three> can pair with ...? <one>Adenine</one>. []
+- A. W. für <one>multibranch loop</one>? <one>Helical junction</one>. URL: https://www.ncbi.nlm.nih.gov/pubmed/11131562 []
+- What is <one>the initial step in E. coli mRNA-degradation</one>? The removal of pyrophosphate from the 5' terminus, leaving a <one>single phosphate</one>.
+- Nenne die Vorläufer zu <one>Purin</one> und <one>Pyrimidin</one>. A: <one>Inosinsäure</one> und <one>Uridylat</one>. []
+- <one>Which sugar</one> can we find within DNA? <one>2-prime deoxyribose</one>. []
+- Where were <one>small, non-coding RNAs</one> initially discovered? In <one>plants</one>. []
+- Name an algorithm to <one>solve the RNA folding problem</one>, starting with <three>N</three>. A: The <one>Nussinov-Jacobson Algorithm</one>, a dynamic programming algorithm. []
+- Eine <one>Deaminierung von Methylcytosin</one> ergibt? <one>Thymin</one>. []
+- Associated with <three>group I introns</three>, what is <one>Twort</one>? A <one>bacterial phage</one>. URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC22036/ []
+- Ist <one>Hypoxanthin</one> ein <three>Purinderivat</three> oder ein <three>Pyrimidinderivat</three>? <one>Hypoxanthin</one> ist ein <two>Purinderivat</two>. []
+- Which year was the <one>breakthrough</one> for <three>small RNAs</three>? <one>2002</one>. []
+- The <one>SAM-sensing riboswitch</one> has how many different states? (1) a state that <one>can bind SAM</one> (2) a state that <one>can NOT bind SAM</one> []
+- What is the <one>trigger molecule of RNAi</one>? <one>dsRNA</one>. []
+- Give a specific example for a <one>Non-Watson - Crick base pairing</one>. A: The <one>G-U wobble</one> base pair. []
+- Name a protein that <one>assists the tmRNA</one>. A: <one>SmpB</one>. URL: https://www.uniprot.org/uniprot/P0A832 []
+- Nenne ein Enzym das im <one>salvage-pathway</one> für die Synthese von Nukleotiden wichtig ist. A: <two>HGPRT</two> (<one>Hypoxanthin-Guanin-Phosphoribosyltransferase</one>).
+- The default DNA <one>super-coiling</one> in DNA is ... ? Exceptions? <one>Negative supercoiling</one> - <two>except for some viruses of Archaea</two>. []
+- Chemisch betrachtet ist <one>Aciclovir</one> ein Derivat ... welcher Nukleinbase? <one>Guanin</one>. URL: https://en.wikipedia.org/wiki/Aciclovir []
+- What is the simplest <one>RNA folding algorithm</one>? The <one>Nussinov algorithm</one>, developed in the year <two>1978</two>. It determines the maximum number of base pairs that a structure of a sequence S can have. []
+- Give an example for <one>naturally occurring RNA aptamers</one>. A: <one>Riboswitches</one>. URL: https://en.wikipedia.org/wiki/Riboswitch []
+- In <royalblue>A-DNA</royalblue>: how many nucleotide pairs per turn? We will see <two>11 nucleotide pairs per turn</two> in <one>A-DNA</one>. []
+- Gibt es <one>Allosterie</one> bei Ribozymen? Ja. []
+- Is <one>Uracil</one> a purine? No; it is <one>a pyrimidine</one> (just like Thymine). []
+- <one>Riboswitches</one> are often found in mRNAs encoding proteins involved in ... ? <one>Importing important cellular metabolites</one>.
+- A <one>RNA aptamer</one> is typically composed of <three>which two domains</three>? (1) the <one>aptamer domain</one> (2) the <one>expression platform</one>
+- What is <three>the average weight</three> for a <one>tRNA</one>, in <two>kilo-Dalton</two>? <one>25 kDa</one>. []
+- Wozu dient die <one>RNA Interferenz</one> in einem Organismus ursprünglich? A: Dem <one>Schutz des Genoms vor Transposition</one>.
+- <one>Cis-acting signals</one> within a given mRNA are hugely important for proper RNA localization. Give a simpler term for these signal sequences. A: <one>Zip-codes</one>.
+- <one>Durchmesser der DNA-Doppelhelix</one>, in <three>Angstrom</three>? <one>20 Angstrom</one>. []
+- Welcher Faktor trägt wesentlich zur <one>Schmelztemperatur der DNA</one> bei? Der <one>GC-Gehalt dieser DNA</one>. []
+- In RNA secondary structure: a <one>pseudoknot</one> is formed by base pairing between ... ? <one>A single-stranded region of RNA and a loop</one>.
+- <one>Regulatory elements</one> in a mRNA can usually be found where? In the <two>3' UTR</two> (<one>untranslated region</one>). URL: https://en.wikipedia.org/wiki/Three_prime_untranslated_region []
+- Wann oder wo mögen wir die <one>Z-Form</one> sehen? In <one>(GC)n-repetitiven Sequenzen</one>.
+- In <three>RNA secondary structure</three> we can see the <one>kissing loop complex</one>. What kind of structure is this? It is <one>a base pairing interaction</one> between two RNA loop sequences.
+- Is a <one>cytidine</one> or a <one>cytosine</one> larger? The <one>cytidine is larger</one>; it includes the sugar component, as it is a nucleoside. []
+- Was heisst es wenn wir sagen das der genetische Code eindeutig ist? Jedes Codon spezifiziert nur eine einzige Aminosäure. []
+- Wie nennen wir die grosse und kleine Furche der DNA auf englisch (aber nicht <one>'groove'</one>)? (1) <one>small furrow</one> (2) <one>large furrow</one> []
+- Welche allgemeine Sequenzfolge gilt in der <one>Z DNA</one>? Purinbasen wechseln sich mit Pyrimidinbasen ab. []
+- Do <one>Telomerase RNPs</one> exist? Yes they do exist. []
+- <one>RGG repeats</one> are often separated by .... amino acids. A: <one>Aromatic amino acids</one>. []
+- Atomar betrachtet: wie unterscheidet sich <one>Adenin</one> (<two>A</two>) von <one>Guanin</one> (<two>G</two>)? Guanin hat ein <violet>O</violet> (Sauerstoffmolekül), Adenin nicht.
+- What do the <one>gRNAs</one> do? They <one>modify eukaryotic RNAs</one>.
+- Is <one>exogenous mRNA</one> immunostimulatory? Yes. []
+- What means <one>proof reading</one> of tRNA? Only mature tRNA with correct 5-prime and 3-prime are exported into the cytoplasm.
+- Welchen Zucker finden wir in <one>DNA</one>? Den Zucker <one>Desoxyribose</one>, eigentlich <two>D-Desoxyribose</two>. URL: https://de.wikipedia.org/wiki/Desoxyribose []
+- In den <one>Purin-Nukleotiden</one>: an welchen Positionen findet man <three>N</three> (<three>Stickstoff</three>) im Gerüst? <one>N1</one>, <one>N3</one>, <one>N7</one>, <one>N9</one>. []
+- Die <one>Desaminierung von Adenin</one> ergibt ... ? <one>Hypoxanthin</one>. []
+- Die große und kleine Furche in der DNA entstehen durch ... Ausrichtung der Basenpaare. A: <one>Unsymmetrische</one>.
+- Sind <one>Nukleotid-Ketten</one> polar? Ja. Sie <one>haben verschiedene Enden</one>. []
+- A. W. für <one>denaturation sites</one> in <three>DNA</three>? <one>AT-rich sites</one>. []
+- In bacteria: many <one>ARE-binding proteins</one> bind to which other important protein? The <one>exosome</one>. URL: https://en.wikipedia.org/wiki/Exosome_complex
+- <cadetblue>rRNAs</cadetblue> von Wirbeltieren enthalten welches ungewöhnliche Nukleotid? <one>Pseudouridin</one>. []
+- <one>Thymidin</one> besteht, in Kurzform, aus welchen zwei Komponenten? <one>Thymin</one> + <one>Pentose</one>.
+- Give <two>an example</two> for a RNA that is both a <one>ribozyme</one> and a <one>riboswitch</one>. A: <one>GlmS</one>. URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3075592/ []
+- How is <one>the precursor of mRNA</one> called? <one>hnRNA</one>. []
+- <one>RNA Editing bei Säugern</one> wird katalysiert durch ... welche Enzyme? Die <one>Desaminasen</one>. URL: https://de.wikipedia.org/wiki/Adenosin-Desaminase
+- Size range of <one>piRNAs</one> (from-to)? <one>24-30 nucleotides</one>.
+- Ist <one>Uracil</one> oder <one>Thymin</one> leichter? <two>Uracil</two> ist leichter als <two>Thymin</two>. Uracil hat eine <one>H-Gruppe</one>; Thymin hingegen hat an dieser Stelle eine <one>CH3-Gruppe</one>. []
+- Wie lange sind die <one>snRNAs</one> typischerweise? Etwas weniger als <one>200 Nukleotide</one> lang.
+- <one>Defects in the formation of RNPs</one> lead to <three>RNP ... diseases</three>. A: <one>RNP hypo-assembly diseases</one>.
+- <cadetblue>Hydroxylionen</cadetblue> können mit den Basen der DNA wechselwirken. Welche Position ist gefährdet? A: <one>N-1 bei Guanin</one>. []
+- Can <one>RNA editing enzymes</one> also affect <three>DNA molecules</three>? Yes. []
+- What was the big idea for <one>treating diseases via RNAi</one>? <one>Oncogenes</one> are overexpressed in many cancer cells, so it makes sense to try to inactivate these specific genes.
+- <one>Dicer</one> belongs to which family? To the <one>RNase III family of nucleases</one>.
+- Welches Nukleotid trägt eine <one>Methylgruppe</one>? <one>Thymin</one>. URL: https://en.wikipedia.org/wiki/Thymine []
+- <one>How many C-atoms</one> can we find in a <three>Ribose</three>? <one>5</one>. []
+- Wie werden <one>Aptamere</one> produziert? Mit Hilfe von <one>SELEX</one>. []
+- <one>Uracil</one> hat wieviele N-Atome in seinem Ring? <one>2</one>. URL: https://en.wikipedia.org/wiki/Uracil []
+- What do we mean with <one>cis-splicing</one>? This refers to the regular splicing of <one>nuclear RNA encoding proteins</one>.
+- Can a <one>Ribozyme</one> catalyze C-S bond formation? Yes. []
+- Ist die <one>Z-DNA</one> Form der DNA linksgängig oder rechtsgängig? <two>Z-DNA</two> ist <one>linksgängig</one>. []
+- What is <one>a bulge loop</one> in a RNA? A <one>bulge loop</one> consists of unpaired nucleotides in one part of the RNA, whereas the other part that is bound to the secondary structure of said RNA molecule shows contiguous base pairing.
+- Give one specific example of a protein in which we may be able find the <one>RRM-motif</one> (RNA-recognition motif). A: In the <one>U1A protein</one>.
+- Can <one>riboswitches</one> detect <three>uncharged tRNA</three>? Yes. []
+- May <one>mRNA molecules</one> contain <three>modified bases</three>? Yes. []
+- Nenne drei verschiedene Beispiele wo wir <one>kleine Ribozyme</one> häufig finden können. A: (1) <one>Viroide</one> (2) <one>Virusoide</one> (3) <one>Satellitenviren</one>
+- Kann <one>Uracil</one> in DNA vorkommen? Ja. []
+- In <one>RNA Biology</one>: what is meant with the abbreviation <two>RBD</two>? <one>RNA binding domain</one>. URL: http://www.ebi.ac.uk/interpro/entry/IPR035979 []
+- The <one>precursor of mRNA</one> is ... ? <one>hnRNA</one>. URL: https://en.wikipedia.org/wiki/Primary_transcript []
+- The <one>H1 RNA</one> can be found in which component? The H1 RNA is part of the <tomato>RNase P</tomato> complex.
+- Angenommen wir finden <one>G-U</one> in einer RNA. Wo ist G-U stabiler: in der Mitte der Helix oder am Ende einer Helix? Am <one>Ende einer Helix</one>. []
+- Hat die <one>Z-DNA</one> mehr oder weniger Windungen als die <two>A-DNA</two>? Die <one>Z-DNA</one> hat mehr Windungen, und zwar <two>12</two>; die <one>A-DNA</one> hat <two>11</two> Windungen. []
+- What is <royalblue>the principal form of DNA</royalblue> that occurs in natural systems? <one>B-DNA</one>. []
+- <cadetblue>Oligonukleotide</cadetblue> haben eine maximale Kettenlänge von etwa ... ? <one>50 Basen</one>. []
+- Woher stammt die <one>Methylgruppe von Thymin</one>? Vom Cofaktor <one>THF</one> (<two>Tetrahydrofolate</two>).
+- How are <one>the monomers in DNA</one> connected to one another? Via <one>phosphodiester bonds</one>. []
+- What is meant with the term <one>RNA Processing</one>? This refers to <one>every modification made to the primary RNA transcript</one>.
+- Was meinen wir mit <one>Northern Pucker</one> und <one>Southern Pucker</one>? (1) <one>Northern Pucker</one>: die 2'-Hydroxyribose bevorzugt die "C3'-endo Konformation" (2) <one>Southern Pucker</one>: die 2'-Desoxyribose  bevorzugt die "C2'-endo Konformation"
+- Gegeben seien zwei chemische Strukturformeln von <cadetblue>Cytosin</cadetblue> und <cadetblue>Thymidin</cadetblue>. Wie kann ich die beiden schnell unterscheiden? Suche nach der <one>Methylgruppe</one> - ist diese gegeben so muss es <two>Thymidin</two> sein. []
+- Give a specific example for a <one>a non-Watson-Crick base pair in RNA</one>. A: A <one>G:U base pair</one>. []
+- Die <one>Ribose</one> hat n OH Gruppen, wohingegen die <one>Deoxyribose</one> wieviele OH Gruppen besitzt? (1) Die Ribose hat <one>4 OH Gruppen</one>. (2) Die Desoxyribose hat <one>3 OH Gruppen</one>. []
+- <two>Purine</two> haben <one>n Stickstoff-Atome</one>? <one>4</one>. Adenine und Guanine haben jedoch eine NH2 Gruppe, und somit in Summe 5 Stickstoff-Atome. []
+- <three>Welche Person</three> schlug die <one>RNA-Welt</one> vor, basierend auf den Theorien von <two>Carl Woese</two>? <one>Walter Gilbert</one>. URL: https://de.wikipedia.org/wiki/Walter_Gilbert []
+- <one>Splicing</one> requires <three>n steps</three>? <one>2</one>. []
+- What are <one>piRNA</one> effectively doing? They mediate the <one>silencing of genes encoding PIWI-proteins</one>.
+- Ähnelt <cadetblue>Adenosine</cadetblue> eher RNA oder DNA? <one>RNA</one>, da es eine OH-Gruppe an Position 2-prime hat. URL: https://upload.wikimedia.org/wikipedia/commons/thumb/5/53/Caffeine_and_adenosine.svg/1280px-Caffeine_and_adenosine.svg.png []
+- What do we mean with <one>circRNA</one>? This is simply <one>circular mRNA</one>. URL: https://en.wikipedia.org/wiki/Circular_RNA []
+- Does <one>minor splicing</one> occur in humans? Yes - about 700-800 genes in the human genome contain introns that <one>undergo minor splicing</one>. []
+- What do we mean with <one>N-nucleotides</one>? These are <one>nontemplated nucleotides</one>.
+- Do <one>rRNA genes</one> contain introns? Yes - at the least sometimes. []
+- Die Konformation der glykosidischen Bindung in <one>B-DNA</one> ist <three>syn</three> oder <three>anti</three>? <one>Anti</one>. []
+- Wieviele <one>-C=O Gruppen</one> besitzt <three>Uracil</three>? <one>2</one>. []
+- Wenn wir ein <one>Adenosin</one> sehen, wie nennen wir dieses Biomolekül? Adenosin ist ein <one>Nukleosid</one>. URL: https://de.wikipedia.org/wiki/Nukleoside []
+- Zahl der Basenpaare pro Windung in der <one>Z-DNA</one>? <one>12</one>. []
+- Die <one>kleinste eukaroyte rRNA</one> ist ... ? Die <one>5S-rRNA</one>. []
+- The <cadetblue>AU-rich elements</cadetblue> can typically be found where in a mRNA? In the <one>3' untranslated region (UTR)</one> of that mRNA. []
+- <one>DNA</one> is a <three>major contributor</three>? Yes - to the <one>global phosphorous cycle</one>. []
+- Welche <one>Nukleotide in der DNA</one> besitzen eine <violet>Aminogruppe</violet>? (1) <one>Adenin</one>  (<two>A</two>) (2) <one>Cytosin</one> (<two>C</two>)
+- Der <one>salvage pathway</one> für Nukleotide geht über <three>welches Nukleotid</three>? <one>Thymidin</one>. URL: https://de.wikipedia.org/wiki/Desoxythymidin []
+- Dringen <one>Nukleinsäuren</one> durch die Zellmembran? Nein; es kommt zu keiner Permeation durch eine intakte Zellmembran. []
+- Ist <one>Deoxyribose</one> eine <three>Ribose</three>? Ja. []
+- <one>Uracil</one> kann mit welchen Basen eine Paarung eingehen? Mit <one>A</one> (<two>Adenin</two>) und mit <one>G</one> (<two>Guanin</two>). []
+- Individual <one>RNPs</one> can assemble into a variety of higher order structures, generally referred to as ... ? <one>RNP granules</one>.
+- Was meinen wir mit <one>Watson-Crick</one> bei der DNA? Dies sind Basenpaarungen zwischen einem <one>Purin</one> und einem <one>Pyrimidin</one> jeweils.
+- Is the <one>Z-DNA</one> known to occur in nature? Yes. []
+- Given the <one>alphabet {A,T,G,C}</one>, how many <cadetblue>different trinucleotides</cadetblue> are there? 4 ** 3 = 64, thus <one>64 trinucleotides</one>. []
+- In der <three>Z-Form der DNA</three>: welche <one>Nucleotid-Folge</one> finde ich hier besonders häufig? <one>GCGCGCGCGC</one>. []
+- Are <one>lncRNAs</one> polyadenylated? Some are; others are not. []
+- A <one>single nucleotide</one> has a molecular mass of ... n Dalton? <one>330 Da</one>. []
+- <one>scaRNAs</one> can be found where? In <one>Cajal bodies</one>.
+- Abstand innerhalb einer <cadetblue>minor grove</cadetblue> und <cadetblue>major grove</cadetblue> in DNA? (1) <one>minor groove</one>: <two>12 Angstrom</two> (2) <one>major groove</one>: <two>22 Angstrom</two> []
+- Wieviele <one>Doppelbindungen</one> hat ein <three>Purin</three>? <one>4</one> - wobei bei Guanin eines davon als C=O Gruppe vorliegt. []
+- The <one>ASH1 mRNA</one> is transported to ...? The <one>bud tip of yeast cells</one>.
+- Wie definieren wir die Stabilität der RNA-Moleküle in einer Zelle? Über deren <one>Halbwertszeit</one>. []
+- Some mRNA can form a <one>lariat</one> structure. Give another two-word name for the term lariat. A: A <one>cowboy's lasso</one>. []
+- <three>At which pH</three> does DNA become <one>fully denatured</one>? At a <one>pH of 11.3</one>.
+- A <one>RNA recognition motif</one>, as a <two>domain</two>, usually has about ... how many aminoacids? About <one>80</one>.
+- Welches <one>Kation</one> kann <three>Sekundärstrukturen der RNA</three> stabilisieren? <one>Mg2⁺</one>. []
+- Do <cadetblue>mRNA decay pathways</cadetblue> exist in both the nucleus and the cytoplasm of eukaryotic cells? Yes. []
+- Average half-life of a mRNA in <one>E. coli</one>? <one>Less than 5 minutes</one>.
+- Which two specific effects can we achieve by <one>U RNA Editing</one>? (1) <one>new start codon</one> (2) <one>new stop  codon</one>
+- Which <one>nucleotide</one> dominates in <three>spliceosomal snRNAs</three>? <one>Uracil</one>. URL: https://en.wikipedia.org/wiki/Nucleotide []
+- Bei der (de-novo) <one>Biosynthese der Pyrimidinnukleotide</one> liefert Carbamyolphosphat ein N und ein C. Die restlichen 3 C und 1 N werden von welcher Aminosäure bereit gestellt? Von <one>Aspartat</one>. URL: https://viamedici.thieme.de/api/images/l/b/r/i/e/f/bioch_023600_steckbrief.png []
+- In <one>bacteria</one>: <two>which RNA</two> carries out the <three>peptide-bond formation</three> during translation? The <one>23S rRNA molecule</one>. URL: https://en.wikipedia.org/wiki/23S_ribosomal_RNA []
+- Die Abkürzung <one>pRNA</one> steht für ... ? <one>Promoter-associated RNAs</one>. URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3929421/
+- Wie wird aus 2-prime deoxyribose eigentlich ein Nucleotide, wie <one>dAMP</one>? Durch Entfernen von 2x H2O.
+- Why is the <one>CA site</one> so important for eukaryotic Poly A-tail generation? So that the growing RNA is cut just beyond the CA site, by the <one>cleavage factor</one>.
+- What was <one>the first catalytic RNA</one> that was described? The <one>rRNA precursor in Tetrahymena</one>.
+- What is the task of the enzyme <one>dicer</one>? "Dicer" is an enzyme that cleaves "double-stranded RNA" (dsRNA) and pre-microRNA (pre-miRNA) into short double-stranded RNA fragments called "small interfering RNA" (siRNA) and "microRNA", respectively.
+- Nenne die beiden Familien in Säugetierzellen, die sich mit <one>RNA Editing</one> beschäftigen. A: (1) <one>ADAR   Familie</one> (2) <one>APOBEC Familie</one>
+- Bei DNA: was meinen wir mit der <one>syn-Konformation</one> beim Zucker? Das ist dann der Fall wenn die Base im wesentlichen über dem Zuckerring liegt.
+- Nenne die 4 Nucleotideinheiten der DNA. A: (1) Desoxyadenylat (2) Desoxyguanylat (3) Desoxycytidylat (4) Thymidylat

data/lib/studium/exam_topics/rna_seq

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+# =========================================================================== #
+# === RNA-SEQ TAG
+#
+# Everything about the RNA seq technology.
+# =========================================================================== #
+
+- <one>RNA-Seq</one> allows <three>computational reconstruction of the original</three> ... ? <one>RNA transcript</one>.
+- Can we use <one>RNA-seq</one> to <two>investigate alternative splicing</two>? Yes. []
+- Give another word or expression for <one>RNA-seq</one>. A: <one>Deep sequencing of RNA</one>.
+- Benötigt DNA-Seq DNA? Ja, in Form von <one>cDNA</one>. URL: https://www.biostars.org/p/54969/
+- <one>RNA-Seq</one> was introduced in which year? <one>2008</one>.