studium 0.18.7

data/lib/studium/exam_topics/databases_and_sql

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+# =========================================================================== #
+# === Databases
+#
+# Everything about computer-databases, including SQL.
+# (In german: "Datenbanken")
+# =========================================================================== #
+
+- How does <one>PostgreSQL</one> <two>call different users that can connect to its database</two>? <one>Roles</one>. []
+- <one>To initialize a database cluster</one> <two>in PostgreSQL</two>, <three>what command do we use</three>? <one>initdb</one> - see https://www.postgresql.org/docs/current/app-initdb.html []
+- <one>Informix</one> has been created by which company? <one>IBM</one>.
+- Do <one>databases</one> <two>have views</two>? <one>Yes</one>.
+- <one>How</one> do we <two>add data into a SQL-database</two>? Through <one>insert statements</one>.
+- The first databases, back in the 1950s, suffered in particular from which problem? From <one>redundancy problems</one>.
+- <one>Welche Person</one> war <two>eminent wichtig für das relationale Datenmodell</two>? <one>Edgar F. Codd</one>. URL: https://en.wikipedia.org/wiki/Edgar_F._Codd
+- In databases, for the ER model, the basic concept is the <one>entity</one>. <two>What is an entity in this parlance</two>? An <one>entity</one> is <two>a thing or object in the real world with an independent existence</two>.
+- In databases we know the <one>ER model</one>. This ER model puts entities at its core. Each entity has attributes. What are attributes in this context? <one>Attributes</one> are <two>the particular properties that describe it</two>.
+- Bei einer Datenbank, deren <one>Speicherplatz</one> betreffend: nenne ein wichtiges Ziel das hier verfolgt wird. A: Wir möchten die Information möglichst kompakt speichern.
+- Nenne <one>ein Beispiel für ein dokumentoriertes Datenbankmodell</one>. A: <one>XML</one>.
+- Bei <one>Datenbanken</one>: nenne ein anderes Wort für das <two>Ende einer Sitzung</two>. A: Das <one>Ende der Transaktionen</one>.
+- Was meinen wir mit einem <one>Dateisystem</one>, verglichen mit einem <one>Datenbanksystem</one>? In einem <one>Dateisystem</one> wird die Information persistent in Dateien gespeichert, die durch das Betriebssystem verwaltet werden.
+- Wie in jeder systematischen Entwurfsmethodik beginnt man auch im Datenbankentwurf mit der ... ? <one>Anforderungsanalyse</one>.
+- <one>Postgre</one> has a file called <two>pg_hba.conf</two>. What means <three>hba</three>? <one>Host-based authentication</one>.
+- Bei Datenbanken: wie könnten wir den deutschen Begriff <one>Datenanfrage</one> ins Englische übersetzen? <one>Retrieval</one>.
+- Informationen sind der ... des Informationszeitalters. A: Der <one>Rohstoff</one>.
+- Bei Datenbanken gibt es Tupel. Die <one>Anzahl der Tupel</one> wird <two>Kardinalität einer Relation</two> genannt. <three>Was wissen wir weiters wenn wir Tupel sehen</three>? Das <one>Tupel nicht doppelt vorkommen dürfen</one>.
+- Bei Datenbanksystemen: was ist mit dem Begriff <one>Persistenz</one> gemeint? Das <one>Daten in der Datenbank über die Ausführungszeit von Anwendungsprogrammen hinaus erhalten bleiben</one>.
+- Nenne einen <one>SQL-Wert</one> der <two>in Java</two> nicht vorhanden ist. A: Der SQL-Wert <one>NULL</one>.
+- Nenne <one>vier verschiedene Datenmodelle</one> (als Tipp: sie beginnen mit den Buchstaben <two>H</two>, <two>N</two>, <two>R</two> und O). A: (1) <one>Netzwerkmodell</one> (2) <one>Hierarchisches Modell</one> (3) <one>Relationales Modell</one> (4) <one>Objekt Orientiertes Datenmodell</one>
+- In SQL: name <one>the difference</one> between <two>VARCHAR</two> and <two>CHAR</two>. A: <one>Varchar</one> is of variable length, char is of fixed length (and has better performance).
+- In einer Datenbank <one>überleben</one> Daten das Ende von ... ? <one>Transaktionen</one>.
+- In database systems: <one>attributes</one> that <two>are not divisible are called ... </two>? <one>Atomic attributes</one>.
+- <one>How</one> can we make a comment in SQL statement? We use two - (dashes), such as <two>--</two>.
+- Ist ein <one>Datenmodell</one> <two>analog zu einer Programmiersprache</two>? <one>Ja</one>.
+- Die <one>atomaren Verarbeitungsvorgänge in Datenbankverwaltungssystemen</one> werden <two>... genannt</two>. A: <one>Transaktionen</one>.
+- Give an example for a <one>WHERE clause</one> used, <two>in SQL</two>. A: <one>SELECT * FROM Customers WHERE Country='Mexico';</one>
+- <one>How</one> can we fetch large amounts of data from flat files into a SQL database? Via <one>COPY from '</one>/<one>bla</one>/<one>foo.txt'</one>
+- Wofür steht die Abkürzung <one>SQL</one>? <one>Structured Query Language</one>. URL: https://en.wikipedia.org/wiki/SQL
+- Are <one>databases</one> <two>Input</two>/<two>output-intensive</two>? <one>Yes</one>.
+- Sind <one>Datenbanken</one> <two>Ein-</two>/<tow>Ausgabe-intensiv</two>? <one>Ja</one>.
+- Nenne <one>ein Ziel oder einen Verwendungszweck von Datenstrukturen</one>. A: Datenstrukturen dienen zur Verwaltung großer Mengen ähnlicher Objekte.
+- In <one>relationalen Datenbanken</one> gilt das eine Relation eine Menge von Tupeln ist. Was meinen wir damit? Das die Zeilen voneinander verschieden sein müssen.
+- <one>Ein Datenmodell</one> besteht allgemein aus <two>welchen zwei Teilsprachen</two>? (1) der <one>Datendefinitionssprache</one> (2) der <one>Datenmanipulationssprache</one>
+- <one>SQL</one> became an <two>ISO standard</two> in which year? In <one>1987</one>.
+- Ein sehr wichtiger Grund wieso Datenbanken verwendet werden, kann mit dem Stichwort <one>Redundanz</one> begründet werden. <two>Was ist mit diesem Begriff gemeint</two>? Das man nicht die gleiche Information mehrmals speichert, wie zum Beispiel in verschiedenen Dateien.
+- In <one>SQL</one>: <two>How to do a calculation such as 21+21</two>? <one>SELECT 21+21;</one>
+- Bei Datenbanken gibt es <one>Sicherheitsobjekte</one>. <two>Was meinen wir damit eigentlich</two>? <one>Daten</one>.
+- In <one>JDBC-URL</one> haben wir Strings wie zum Beispiel <two>jdbc:oracle:thin:@vier.cs.univie.ac.at:1521:o10g</two>. <three>Was bedeutet 1521 hier</three>? Dies bezeichnet den <one>Port</one>.
+- A <one>database</one> may reflect the world. <two>What would be a slightly better expression here</two>? A <one>database</one> may reflect the <two>miniworld</two>.
+- Eine Programmiersprache wie <one>Java</one> setzte den im Jahre <one>1992</one> entwickelten ODBC Standard um. <two>Wofür steht die Abkürzung ODBC hier</two>? <one>Open DataBase Connectivity</one>.
+- The <one>data</one> in a <two>Relational Database Management System</two> (<three>RDBMS</three>) is stored how? It is stored in database objects called a <one>table</one>.
+- In einem <one>relationalen Datenmodell</one>: der <two>Fremdschlüssel</two> bezeichnet was beziehungsweise hat welche Funktion? Der <one>Fremdschlüssel</one> verweist auf den <two>Primärschlüssel</two> einer anderen Tabelle der Datenbank.
+- In SQL: <one>How to display the current settings for SQL</one>? Via: <one>.show</one>
+- Name <one>the seven major SQL commands</one>. A: (1) DELETE (2) INSERT (3) SELECT (4) UPDATE (5) WHERE (6) <one>DROP</one> (7) <one>CREATE</one>
+- <one>Wann</one> erschien <two>SQL</two>? <one>1974</one>.
+- Can a <one>random assortment of data</one> <two>be called a database</two>? <one>No</one>.
+- Die älteste DBMS-Kategorie ist seit 1968 auf dem Markt. Der populärste Vertreter ist <one>IMS</one>/<one>VS</one> (<two>Information Management System</two> / <two>Virtual Storage</two>), von welcher Firma? <one>IBM</one>. URL: https://en.wikipedia.org/wiki/IBM_Information_Management_System
+- <one>NoSQL</one> is <two>an abbreviation</two> for ... ? <one>not only SQL</one> URL: https://en.wikipedia.org/wiki/NoSQL
+- Does <one>SQL</one> have <two>VARBINARY</two>? <one>Yes</one>.
+- <one>When</one> do we use the <two>UPDATE</two> command in SQL? When we wish to update data in a table.
+- In <one>SQL</one>: <two>how do we exclude conditions</two>? Via <one><></one>.
+- Name <one>two common operations on a database</one>. A: (1) <one>retrieval</one> <two>of data</two> (2) <one>update</one>    <two>of data</two>
+- Was meinen wir mit einem <one>Vektor</one>, bei einer Datenbank? Ein <one>Vektor</one> <two>verwaltet eine fix vorgegebene Anzahl von Elementen eines einheitlichen Typs</two>.
+- In a database: <one>when</one> may <two>a lot of data be queried simultaneously</two>? When many users try to process the data simultaneously too, that is at the same time.
+- In <one>SQL</one>: <two>how to do a conditional query</two>, in general? Via <one>WHERE condition;</one>
+- What do we mean with <one>a database application</one>? A database application refers to a particular database and the associated programs that implement the database queries and updates.
+- <one>Datenbanken sollten sicher sein</one>; <two>Datensicherheit ist wichtig</two>. Gib ein Beispiel für den Begriff Datensicherheit in dieser Hinsicht. A: <one>Schutz vor unberechtigtem Zugriff</one>.
+- Wie aktivieren wir <one>headers</one> in sqlite? Via: <one>.headers on</one>
+- In databases, the <one>ER model</one> is very popular. What does <one>ER</one> stand for? <one>Entity-relationship</one>.
+- Bei Datenbanksystemen hat sich eine <one>Drei-Ebenen-Architektur</one> durchgesetzt. <two>Welche sind dies</two>? (1) die <one>externe</one> Ebene (2) die <one>konzeptuelle</one> Ebene (3) die <one>interne</one> Ebene
+- Bei den <one>relationalen Datenbanken</one>: in Tabellen-Darstellung sind die Attributnamen ... ? die <one>Spaltenüberschriften</one>.
+- How can we <one>avoid NULL</one> in SQL? By using <one>NOT NULL</one>.
+- <one>DBAs</one> is an abbreviation for ... ? <one>Database administrators</one>.
+- What is a <one>database cluster</one>? A: This is <one>database storage area on a disk</one>.
+- In SQL: Why do we use the <one>SELECT DISTINCT</one>? To <one>remove duplicate rows</one>.
+- <one>Databases</one> uses <two>ACS</two>. <three>What does this abbreviation stand for</three>? <one>Access control systems</one>. URL: https://en.wikipedia.org/wiki/Access_control#Computer_security
+- In Datenbanken sind die Attributwerte <one>atomar</one>. <two>Was ist mit so einer Aussage gemeint</two>? Das sie <one>nicht teilbar sind</one>.
+- Was ist eine <one>Datenbankmanagementsystem</one> (<two>DBMS</two>)? Ein <one>Datenbankmanagementsystem</one> (<two>DBMS</two>) besteht aus einer Sammlung korrelierter Daten (i.e. Datenbank) und Programmen, die darauf zugreifen können.
+- Nenne ein Beispiel für <one>eine Generalisierung der Liste auf eine 2-dimensionale Datenstruktur</one>, die auch bei Datenbanken zur Anwendung kommt. A: Der <one>Baum</one> (<two>tree</two>).
+- Datenbanken verwenden auch <one>Berechtigungssystem</one>. <two>Was soll so ein System unter Umständen verhindern</two>? Das ein <one>Zugriff durch Nichtberechtigte</one> erfolgt; dies wird somit verhindert. Bei jedem Zugriff werden die Berechtigungen überprüft.
+- Beim <one>Datenbankentwurf</one> beginnt man meistens indem man den Ausschnitt aus der realen Welt bestimmt, welcher in der Datenbank modelliert werden soll. <two>Wie nennt man diesen Ausschnitt noch</two>? Dies ist die sogenannte <one>Miniwelt</one>.
+- Ein <one>Datenmodell</one> <two>besteht aus welchen zwei Teilsprachen</two>? (1) der Datendefinitionssprache (2) der <one>Datenmanipulationssprache</one>
+- Anderer Begriff für <one>flüchtige Daten</one>? <one>Transiente Daten</one>.
+- In SQL haben wir das <one>Cursorkonzept</one>. <two>Was ist ein Cursor in diesem Kontext</two>? Ein <one>Cursor</one> ist eine Datenstruktur zum Zwecke des Granularitätsausgleiches zwischen SQL und Wirtssprache.
+- The <one>ER model</one> describes data as ... which three groups? (1) <one>entities</one> (2) <one>relationships</one> (3) <one>attributes</one>
+- How do we call <one>the duplication of data</one>? <one>Data redundancy</one>.
+- PostgreSQL features transactions with <one>ACID properties</one>. <two>ACID means ... </two>? (1) <one>Atomicity</one> (2) <one>Consistency</one> (3) <one>Isolation</one> (4) <one>Durability</one>
+- Der <one>Systemprogrammierer</one> der sich mit Datenbanken gut auskennt und auseinander setzt wird generell ... genannt. A: <one>Datenbankadministrator</one>.
+- Why do we use <one>tablespace</one> in Postgresql? We can define locations in the file system where the file resides.
+- Es gibt in Datenbanken einen sogenannten <one>Oberschlüssel</one>. <two>Wie nennen wir diesen auf englisch</two>? <one>superkey</one>.
+- Nenne zumindest <one>zwei Eigenschaften</one>/<one>Vorteile</one> von <two>DBMS</two> (Database Management Systems). A: (1) <one>Persistenz</one> (2) <one>Mehrbenutzerfähigkeit</one> (3) <one>Datensicherheit</one>
+- Datenbanken waren in der Computer-Geschichte, zumindest früher, oft ähnlich zu welch anderer <one>Datenstruktur</one> aus dem echten Leben? <one>Tabellen</one>. Diese bringen rein wertbasierte Verweise; also eine <two>Relation</two> zu diesen Daten.
+- What purpose does the <one>pg_hba.conf</one> file serve? <one>pg_hba.conf</one> <two>controls client authentication</two>.
+- Gibt es einen Zusammenhang zwischen der Tiefe eines Baumes und der Anzahl der Knoten? <one>Ja</one>, und zwar ein <two>exponentieller Zusammenhang</two>. Je tiefer der Baum ist desto mehr Knoten besitzt er.
+- <one>Welchen Fokus</one> hat <two>ein verteiltes Datenbanksystem</two>? Der Fokus ist <one>die gemeinsame Nutzung der Daten</one>.
+- Ein <one>Datenmodell</one> macht was? Ein <one>Datenmodell</one> legt die Modellierungskonstrukte fest, mittels derer man ein computerisiertes Informationsabbild des relevanten Ausschnitts aus der realen Welt generieren kann.
+- <one>Primärschlüssel</one> werden im <two>Relationenschema</two> wie gekennzeichnet? Sie sind <one>unterstrichen</one>.
+- In SQL: what is meant with the <one>UNIQUE</one> statement? This <one>constraint</one> means that a column ensures that there will not be two identical entries in that column.
+- How can we ensure that we are in the right database? We apply the <one>USE</one> command such as via USE nodes;
+- Was ist die <one>Datenbasis</one>? Als Datenbasis bezeichnet man die in einem DBMS gespeicherten Daten.
+- Dürfen im <one>relationalem Datenmodell</one> Tupel doppelt vorkommen? Nein. <royalblue>Tupel</royalblue> dürfen hier <orange>nicht</orange> doppelt vorkommen.
+- Is SQL <one>case sensitive</one>? No - SQL is case insensitive.
+- Angenommen wir haben eine Datenbank für Telefoneinträge. Wir möchten diese Datenbank nun durchsuchen. Ist die <one>Baumstruktur</one> oder die <one>Hashverwaltung</one> hierbei schneller? Die <one>Hashverwaltung</one> ist schneller und somit effizienter.
+- In <one>PostgreSQL</one>: how do we <two>transfer data between a file and a table</two>? We use <one>COPY FROM</one>, or rather, use <two>\copy</two>.
+- Welches Modell ist der <one>Ur-Vater</one> der <two>semantischen Datenmodelle</two>? <one>ERM</one>: das <one>Entity-Relationship-Modell</one>
+- In der <one>Tabellen-Darstellung</one> sind die Attributnamen ... ? <one>die Spaltenüberschriften</one>.
+- Databases uses transactions. Which <one>state</one> do these prefer? The <one>consistent state</one>.
+- Wenn wir <one>eine lange Liste</one> haben die wir sequenziell durchsuchen, welche einfache Strategie könnten wir verwenden um diese Datenmenge zu reduzieren, für die Suche? Wir könnten <one>binäres Aufteilen</one> verwenden.
+- Nenne ein allgemeines Beispiel für ein <one>dictionary</one>, das auch etwas mit Datenbanken zu tun hat. A: <one>Wörterbücher</one>.
+- What is a <one>relational database</one>? This is <one>a collection of data organized in tables</one>.
+- Was ist mit dem Begriff <one>referentielle Integrität</one> bei (relationalen) Datenbanken gemeint? Dies bezeichnet Regeln, deren Einhaltung beim Eingeben oder Löschen von Datensätzen überprüft werden, um die definierten Beziehungen zwischen Tabellen beizubehalten.
+- Bei Datenbanken: was meinen wir mit einem <one>atomaren Attributwert</one>? Dies ist <one>ein Wert der nicht aus mehreren Werten zusammen gesetzt</one>.
+- Ein <one>Baum</one> (tree), der in Datenbanken Verwendung findet, besteht aus ... ? (1) <one>Knoten</one> (2) <one>Kanten</one>
+- Was ist das primäre Ziel bei einem <one>parallelen Datenbanksystem</one>? Eine <one>Geschwindigkeitsverbesserung</one> - eben durch die parallele Ausführung der Operationen.
+- Was meinen wir mit dem Begriff <one>Fremdschlüssel</one>? Mit Fremdschlüssel bezeichnen wir das Attribut einer Relation, das in einer anderen Relation ein Schlüssel ist.
+- Bei Datenbanksystemen und Normierungsbemühungen: wofür steht die Abkürzung <one>CODASYL</one>? <one>Conference on Data Systems Languages</one>.
+- Was ist mit dem Begriff <one>roll-backward</one> gemeint bei Datenbanken/Datenbanksystemen? Dies meint das die Auswirkungen aller unbestätigten Transaktionen eliminiert werden.
+- Was ist, konkret, mit dem Begriff <one>Transaktion</one> gemeint bei Datenbanken? Dies bezeichnet eine Folge von Aktionen, wie zum Beispiel Lese- und Schreibzugriffe auf die Daten einer Datenbank.
+- Was ist gemeint mit dem Begriff <one>Mehrbenutzerfähigkeit</one> bei Datenbanken? Das mehrere Benutzer gleichzeitig auf die Daten zugreifen und mit diesen arbeiten können.
+- How do we list all databases in <one>postgreSQL</one>? <one>\list</one>
+- Die Sammlung der Information in einem DBMS zu einem Zeitpunkt nennt man ... ? <one>Instanz</one>.
+- <one>Relationen in Datenbanken</one> können auf einfache Weise als ... interpretiert werden. A: Als <one>Tabellen</one>.
+- Die logische Struktur der Information in einer Datenbank nennt man ... ? <one>Schema</one>.
+- Die grundlegende Struktur der in der Datenbank gespeicherten Daten ist ... ? Das so genannte <one>Datenmodell</one>.
+- In einem Datenbanksystem, was meinen wir mit dem <one>Nullwert</one>? Dies ist allgemein ein spezieller Wert, der ausdrückt, dass kein Wert angegeben ist (da dies für diesen Eintrag in der Datenbank, zum Beispiel, unbekannt ist).
+- When designing a database, why should we separate the first and the last name into separate fields? This simplifies data searching and sorting.
+- In SQL, how to delete a database? dropdb

data/lib/studium/exam_topics/dna_mutation_and_dna_repair

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+# =========================================================================== #
+# === DNA Mutation and DNA Repair
+#
+# Everything about DNA mutation and DNA repair can be collected in this
+# file here.
+# =========================================================================== #
+
+- Name a very important <one>sub-pathway of NER</one>. A: The TC-NER: <two>transcription-­coupled NER</two>.
+- For a cell to initiate a DNA repair reaction, it is crucial to sense the existence of a relevant ...? <one>lesion</one> in the DNA.
+- Die 3'-5'-Exonuclease der DNA-Polymerase I in Escherichia coli entfernt nur welche Nukleotide? Nur ungepaart vorliegende Nukleotide.
+- Die <one>Desaminieren von Cytosin</one> konvertier eine ...-gruppe in eine ---gruppe. A: Eine Aminogruppe in eine Ketogruppe.
+- <one>Human BRCA2 protein</one> <two>promotes ... filament formation</two>. A: <one>RAD51 filament formation</one>.
+- Somatische Mutationen (in Eukaryoten) haben eine größere Wirkung wenn sie dominant sind - oder ... ? bei Männchen, wenn diese Mutationen X-gekoppelt vorliegen.
+- Replikationsfehler aufgrund von Fehlpaarungen führen vor allem zu ... ? <one>Punktmutationen</one>.
+- Das wohl beste, allgemeine Beispiel für konditionale Mutationen sind ... ? <one>Temperatursensitive Mutationen</one>. URL: https://www.u-helmich.de/bio/lexikon/T/Temperatursensitive_Mutationen.html
+- <one>Different organisms</one> <two>vary</two> <one>in their mutation rates</one>. <three>Name one possible explanation as to why that is the case</three>. A: <one>These differences</one> may, in part, <one>reflect the relative efficiencies of different DNA proofreading and repair systems</one>.
+- <one>DNA sequences</one> that appear to <two>be highly susceptible to mutation</two> are also called ... ? <one>Mutation hot spots</one>.
+- Give <one>two specific examples</one> for <two>exogeneous DNA damage</two>. A: (1) cigar smoke creating benzopyrene, which in turn may create bulky adducts onto DNA (2) <one>UV light damage</one>, such as caused from sunlight
+- Are most <one>loss-of-function mutations</one> dominant? <one>No</one>, they are recessive.
+- In der Genetik: wie können wir eine Mutation definieren? Eine <one>Mutation</one> ist <two>eine Veränderung einer DNA Sequenz</two>.
+- Über den Zeitpunkt einer Mutation können welche zwei Einteilungen vorgenommen werden? (1) spontant (2) induziert
+- The <one>BRCA2 protein</one>, important in DNA repair, has approximately how many acids? <one>3418 amino acids</one>.
+- <one>Non-homologous end joining</one> repairs double-strand breaks without using a homologous template. In which cell cylce stage is this pathway usually active? In <one>G1</one>.
+- <one>Mutations</one> that result from the influence of exogenous factors are called ... ? <one>induced mutations</one>.
+- The <one>meiotic homolog of RAD51</one> is ... ? <one>DMC1</one>. URL: https://en.wikipedia.org/wiki/DMC1_(gene)
+- DNA can be damaged by chemical reactions or irradiation. Alternatively, DNA can also be damaged ... how? When DNA is copied during <one>DNA replication</one>.
+- <one>BRCA2</one> <two>interacts with eight conserved motifs</two>, <three>called BRC repeats</three>. These consist of approximately n amino acids? <one>35</one>.
+- <one>Wie</one> erkennt das <two>Mismatch Repair System</two> den alten DNA-Strang? Anhand der <one>methylierten Basen</one>.
+- <one>Which three pathways</one> <two>are available for eukaryotic cells to to repair DSBs</two>? (1) <one>Non-homologous end-joining</one> (NHEJ) (2) Alternative end-joining (aEJ) (3) <one>Homologous recombination</one>
+- <one>5-Bromouracil</one> (in <two>its keto form</two>) <three>can base pair with ... </three>? <one>Adenine</one> (<two>A</two>).
+- The <one>BRCA2 protein</one> can bind which other protein? <one>RAD51</one>.
+- The earliest demonstration of the artificial induction of mutations occurred in 1927, when Hermann Joseph Muller reported that X rays could cause mutations in ... ? <one>Drosophila</one>. URL: https://en.wikipedia.org/wiki/Hermann_Joseph_Muller#Discovery_of_X-ray_mutagenesis
+- Name <one>two different pathways</one> <two>that can repair double-strand breaks</two>. A: (1) <one>Homologous recombination</one> (2) <one>Nonhomologous end joining</one>
+- <one>Direct repair</one> restores the ... ? original structures of nucleotides.
+- <one>Mutations</one> <two>provide the basis for genetic ... </two>? <one>analysis</one>.
+- Geht <one>NHEJ</one> mit einem <two>Verlust an Nukleotiden</two> einher? <one>Ja</one>, fast immer - vor allem an den DNA Enden.
+- The <one>3' ssDNA tail</one> <two>is essential for homologous recombination</two>. Which protein binds to it? <one>Rad51</one>.
+- Im bakteriellen Reparatursystem, beim <one>mut-Reparatursystem</one>: welches Protein erkennt (und bindet) an das falsche Basenpaar? Das <one>MutS-Protein</one>.
+- <one>Artemis</one> can be found in which repair pathway? In <one>NHEJ</one>.
+- <one>Mutations</one> that result in complete loss of function are known as ... ? <one>null mutations</one>.
+- Name <one>the four steps in homologous recombination</one>. A: (1) removal of some nucleotides at the broken ends (2) strand invasion (3) displacement (4) <one>replication</one>
+- Give another name for the term <one>point mutation</one>. A: <one>Base substitution</one>.
+- <one>DNA polymerase β</one> makes how many mistakes per 10000 nucleotides synthesied? A bit more than two mistakes; specifically 1 mistake per 4000 nucleotides.
+- Name <one>a chemical agent</one> <two>that can cause double-stranded breaks</two>. A: <one>Bleomycin</one>.
+- Bei der <one>DNA Exzisionsreparatur</one>: <two>wie nennen wir allgemein jene Proteine, die defekte Bereiche erkennen und rausschneiden</two>? <one>Uvr-Proteine</one>. <two>uvr</two> steht für <three>UV-repair</three>.
+- Provide a <one>specific example</one> <two>how point mutations could lead to the manifestation of a disease in eukaryotes</two>. A: <one>Point mutations</one> can alter mRNA splicing. For instance, a G->T transversion could eliminate the 5' splice site so that the intron would be retained in the mRNA. The Intron boundaries are typically GT-INTRON-AG, so a change from GT to TT would mean that the Intron could no longer be excised.
+- <one>Direct repair</one> can repair what exactly? <one>UV-induced pyrimidine dimers</one>.
+- <one>Direct repair</one> corrects ... which alkylation product of guanine? <one>O6-methylguanine</one>.
+- Die <one>gefährlichste Form von DNA-Schädigung</one> ist ... ? ein <one>DNA-Doppelstrangbruch</one>.
+- Name <one>two enzymes</one> that are used both in the repair of double strand break as well as carrying out crossing over. A: (1) BRCA1 (2) <one>BRCA2</one>
+- <one>DNA end resection</one>, <two>as part of DNA repair</two>, occurs in n steps? In <one>two steps</one>.
+- <one>Cisplatin</one> <two>can induce interstrand crosslinks</two> (ICLs). Name another substance that can also induce ICLs. A: <one>Mitomycin C</one>.
+- How can <one>mismatch repair</one> distinguish between the old and the new DNA strand? By the presence of methyl groups on certain sequences on the old DNA strand.
+- <one>Elektromagnetische Strahlung</one> kann direkt oder indirekt wirken. Nenne ein Beispiel für eine individuelle Wirkung auf eine Zelle. A: Wenn elektromagnetische Strahlung zuerst mit den Wassermolekülen in der Zelle reagieren und dabei Hydroxylradikale gebildet werden.
+- Bei <one>NHEJ</one>: welche Proteine lagern sich an die DNA Enden (initial) an? Ku70/Ku80.
+- If <one>Chd1</one> <two>is deleted in a mouse</two>, what will happen? This deletion will result in <one>embryonic lethality</one>.
+- Are <one>exogenous mutagens</one> more efficient at inducing mutations if a gene is highly transcribed, in bacteria? Yes.
+- Name <one>a specialized NER sub-pathway</one>. A: <one>Transcription-coupled NER</one>.
+- <one>Homology directed repair</one> (<two>HDR</two>) requires what to repair the DNA? A <one>homologous sequence</one> is required.
+- <one>DNA end resection</one> (<two>during DNA repair</two>) occurs in two steps. How are these two steps called, in general? (1) short range step (2) <one>long range step</one>
+- Name <one>an alternative pathway</one> <two>that also repairs DNA</two>, other than Non-homologous end joining (NHEJ). A: <one>Microhomology-mediated end joining</one> (<two>MMEJ</two>).
+- <one>Without mutation</one>, <two>all genes would ... </two>? <one>exist in only one form</one>.
+- Is <one>mutation</one> <two>connected to recombination</two>? <one>Yes</one> - the DNA damage that is <two>a double-strand break</two>, is also an intermediate step in the normal cellular process of recombination, through meiotic crossing over.
+- In patients with Xeroderma Pigmentosum, the risk of mutagenesis is elevated tremendously by a hereditary defect in one of two biological processes: one is the nucleotide excision repair (NER), and the other is ... ? <one>DNA translesion synthesis</one> (<two>TLS</two>).
+- <one>Indels</one> findet man bevorzugt in welchen Bereich im Genom? In <one>DNA-Abschnitten</one> <two>mit kurzen Sequenzwiederholungen</two>, wie zum Beispiel AAAA, CACA oder CAGCAG.
+- <one>Which pathway</one> is the most important one when it comes to the removal of ultraviolet light (UV)-induced DNA photolesions from the genome? NER (Nucleotide excision repair).
+- <one>Which enzyme</one> is <two>the most important one</two> in the DNA <three>base excision repair</three> pathway? <one>Apurinic</one>/<one>apyrimidinic (AP) endonuclease</one>.
+- <one>CHD1</one> <two>promotes MLH1-MLH3 accumulation</two> at ... ? <one>future crossover sites</one>.
+- <one>Translesion DNA polymerases</one> allow replication to proceed past ... in the DNA. A: Past bulky distortions in the DNA.
+- The cause of Xeroderma pigmentosum is ... ? a deficiency in nucleotide excision repair (NER).
+- When distortions of the template in dsDNA are encountered, which DNA polymerase in general correct this problem? The <one>translesion DNA polymerases</one>.
+- The <one>importance of DNA repair in eukaryotes</one> is indicated by the identification of more than ... repair genes in the human genome. A: <one>More than</one> <two>130 repair genes</two> in the human genome.
+- Das Proteindimer Ku70/Ku80 zieht nach Bindung an DNA welche Kinase an? Die DNA-abhängige Proteinkinase (DNA-PKcs).
+- <one>Cyclobunate pyrimidine dimers</one> <two>can be repaired by the enzyme called ... </two>? <one>CPD photolyase</one>.
+- Does <one>BER</one> <two>repair</two> <three>single-strand breaks</three> or <three>double-strand breaks</three>? <one>Single-strand breaks</one>.
+- <one>DNA repair</one> acts to s... t... A: <one>DNA repair</one> acts to <two>suppress tumorigenesis</two>.
+- In nicht-proliferenden eukaryoten Zellen ist der wichtigste Reparaturmechanismus ... ? Die nicht homolge End-zu-End Verknüpfung (NHEJ, aka non-homologous end joining). URL: https://en.wikipedia.org/wiki/Non-homologous_end_joining
+- Warum sind <one>blockierte Replikationsgabeln</one> <two>anfällig gegenüber Endonucleasen</two>? Da sie <one>lange einzelsträngige Bereiche besitzen</one>.
+- <one>Welche Hefe-Mutanten</one> <two>können DSBs nicht reparieren</two>? Die <one>rad-Mutante</one>.
+- Das <one>postreplikative Mismatch-Reparatursystem</one> ist auch zur Reparatur von ... DNA ... ausgerüstet. A: Zur <one>Reparatur von extrahelikalen DNA Schleifen</one> ausgerüstet.
+- Is there <one>a natural role for double-strand breaks</one>? <one>Yes</one> - <two>a double-strand break initiates the crossover event in meiosis</two>.
+- Is <one>MMEJ</one> (<two>microhomology-mediated end joining</two>) more error-prone than the NHEJ pathway? <one>Yes</one>.
+- <one>Non-homologous end joining</one> (NHEJ) is a pathway that can ... ? <one>repair double-strand breaks in DNA</one>.
+- Do double-strand breaks in DNA stall DNA replication? Yes.
+- The homologies required in microhomology-mediated end joining (MMEJ) have a size range of 5 up to ... n bp? Up to 25 bp.
+- How do we in general call transitions and transversions? <one>Substituions</one>.
+- In DNA Repair: the abbreviation <one>ICLs</one> stands short for ... ? <one>Induces interstrand crosslinks</one>.
+- In <one>E. coli</one>: <two>was dient als natürliches Signal für die Mismatch-Reparatur</two>? Die Abwesenheit von methyliertem Adenin in GATC Folen, im E. coli Genom.
+- Is <one>homologous recombination</one> <two>virtually error-free</two>? <one>Yes</one>.
+- <one>Inappropriate NHEJ</one> can lead to translocations and telomere fusion, hallmarks of ... ? <one>tumor cells</one>.
+- The <one>repair pathway</one> called <two>synthesis-dependent strand annealing</two> makes use of which Heterodimer specifically? <one>KU70</one> and <one>KU80</one>.
+- The <one>Bloom syndrome</one> <two>is caused by mutations in the BLM gene</two>, which is a member of which family? Of the <one>RecQ DNA helicase family</one>.
+- <one>Chd1</one> <two>remodels chromatin to promote ... </two>? <one>meiotic crossing-over</one>.
+- <one>Induced mutations</one> <two>arise through the action of ... </two>? <one>mutagens</one>.
+- In the <one>long range DNA end resection pathway</one>, Sgs1, Top3 and Rmi1 form a complex. The Sgs1 there acts as a ... ? <one>3' → 5' helicase</one>.
+- Defects in BLM/Sgs1 lead to ... ? <one>Bloom’s syndrome</one>.
+- BRCA2 displaces ... from dsDNA. A: <one>RAD51</one>.
+- Which protein promotes RAD51 function? <one>BRCA2</one>.
+- <one>Which enzyme</one> <two>initiates homologous recombination</two>? The <one>Rad51 recombinase</one>.
+- Give another, better name for <one>DNA end resection</one>. A: <one>5'→3' nucleolytic degradation of DNA ends</one>.
+- Is <one>deamination</one> <two>more common than</two> <one>depurination</one>? No - deppurination is more common.
+- Is the 3' ssDNA tail essential for homologous recombination? Yes.
+- The decision whether or not to extensively ... dictates the pathway choice in DNA double-strand break repair. A: <one>resect DNA</one>.
+- <one>Welcher Komplex</one> ist beim <two>nonhomologus-end joining</two> aktiv? Die <one>Ku-Heterodimere</one>, die den <two>DNA Schaden erkennen</two>. URL: https://en.wikipedia.org/wiki/Ku_%28protein%29
+- Give another name for <one>error-prone</one>. A: <one>Inaccurate</one>.
+- Is homologous recombination template-dependent? <one>Yes</one>.
+- Homologous recombination is confined to the cell-cycle, in particular which cell cycle boundary? The <one>S/G2 phase</one>.
+- Name the <one>two most frequent spontaneous lesions</one>. A: (1) <one>deamination</one> (2) <one>depurination</one>
+- The <one>human genome</one> contains at the least ... how many <two>translesion polymerases</two>? <one>5</one>.
+- <one>Indels</one> commonly arise, most likely, by a mechanism called ... ? <one>Replication slippage</one>.
+- <one>Base-excision repair</one> is carried out by which enzymes? By <one>DNA glycosylase</one>. They will cleave base-sugar bonds.
+- <one>Homologous recombination</one> <two>plays an important role in regards to DNA damage</two>, via ... ? The so-called <one>recombination repair</one>.
+- In general, alleles with a frequency of greater than n% can be considered to be a <one>wild type</one>. A: Greater than 1%.
+- Is the <one>deamination of guanine</one> <two>mutagenic</two>? <one>No</one>. <two>Deamination of guanine produces xanthine</two>, which also base-pairs with cytosine, just as guanine does.
+- <one>Base excision repair</one> constantly counteracts the ... ? collapse of our DNA.
+- Name <one>a mutation event</one> that can generate mutations but leaves the DNA backbone intact. A: <one>Depurination</one>.
+- <one>Nitrous acid</one> is <two>a potent mutagen</two> that can act on either replicating or nonreplicating DNA. What is its chemical formula? <one>HNO₂</one>.
+- <one>Single-base-pair changes</one> <two>that inactivate proteins</two> <three>are often due to ... </three>? <one>splice site mutations</one>.
+- The <one>photoreactivation repair</one> <two>can repair ... </two>? <one>Dimers</one>, such as <two>Thymidine dimers</two>.
+- What happens in a <one>nonsense mutation</one>? The codon for one amino acid is changed into a stop codon.
+- <one>Mutations</one> that involve changes at specific sites in a gene are referred to as ... ? <one>Point mutations</one>.
+- What does <one>redundancy in DNA repair</one> mean? This means that <one>many types of DNA damage</one> <two>can be corrected by</two> <three>more than one pathway of repair</three>.
+- Probably the most commonly used mechanism of DNA repair in eukaryotes is ... ? <one>Homologous recombination</one>.
+- Name <one>two general problems or diseases</one> associated with <two>DNA repair defects</two>. A: (1) they may <one>cause accelerated aging</one> (2) they may <one>lead to an increased risk of cancer</one>
+- What are <one>DDR pathways</one>? <one>DNA damage response pathways</one>.
+- Name <one>a famous disease</one> that is <two>related to a faulty DNA repair</two>. A: <one>Xeroderma pigmentosum</one>. URL: https://en.wikipedia.org/wiki/Xeroderma_pigmentosum
+- <one>Crossing over</one> is also <two>important in DNA Repair</two>. Normally it takes place between ... ? <one>Two homologous chromosomes</one>.
+- <one>Which repair pathway</one> rejoins broken double-strand ends? The <one>nonhomologous end-joining pathway</one>.
+- <one>Cell death response</one> largely means involvement of ... ? <one>p53</one>.
+- The most potentially serious class of DNA damage is ... ? a <one>double-stranded break</one>.
+- The <one>acridines</one>, which are <two>mutagens</two>, have which electric charge? They are <one>positively charged</one>.
+- <one>Photoreactivation</one> <two>repairs what</two>? <one>Pyrimidine dimers</one>. URL: https://en.wikipedia.org/wiki/Photolyase
+- Die <one>O-6-Methylguanin-Methyltransferase</one> <two>repariert DNA</two>. <three>Was entfernt sie aus der DNA</three>? <one>O-6-Methylguanin</one>. Aus diesem wird wieder ein Guanin.
+- <one>Why</one> can <two>excision repair</two> work? Because <one>the other (undamaged) strand</one> <two>serves as a template</two>.
+- Name the <one>two main types of point mutation</one>. A: (1) <one>base substitution</one> (2) <one>base insertion</one>/<one>deletion</one>
+- Mechanistically, <one>how</one> do <two>DNA glycosylases</two> work? They diffuse laterally along the minor groove of the DNA until a specific kind of lesion is detected.
+- Nenne <one>drei Möglichkeiten</one> wie eine Zelle <two>UV Schäden</two> korrigieren kann. A: (1) <one>Photo-Reaktivierung</one> (2) <one>Nucleotid-Exzisions-Reparatur</one> (<two>NER</two>) (3) <one>rekombinative Reparatur</one>
+- What is <one>the most dangerous DNA damage</one> that also occurs somewhat regularly? A <one>DSB</one> (<two>DNA double-strand break</two>).
+- <one>Welches Enzym</one> entfernt <two>Uracil</two> aus <three>dsDNA</three>? Die <one>Uracil-DNA-Glycosidase</one>. URL: https://www.ncbi.nlm.nih.gov/mesh/68051981
+- <one>When</one> is <two>recombinational repair</two> used? When <one>both strands are damaged</one>, e. g. <two>when the DNA is broken</two>.
+- What is a <one>synonymous mutation</one>? This is when a mutation-event changes one codon for an amio acid into another codon for that same amino acid.
+- Why is the term <one>insertion mutation</one> not extremely accurate? Because they are actually <one>nucleotide-pair insertions</one>.
+- Eine <one>DNA-Mutation</one> kann entstehen durch <two>Methylierung von Guanin</two>, aber an welcher Position? An der <one>O6-Position</one>.
+- The <one>main nuclease</one> <two>in the non-homologous DNA end-joining pathway</two> (<three>NHEJ</three>) in vertebrates is called ... ? <one>Artemis</one>. []
+- Die Erforschung der <one>NER</one> (<two>Nukleotid-Excisionsreparatur</two>) <three>begann mit ... </three>? <one>E. coli Mutanten</one> <two>die empfindlich auf UV-Licht reagieren</two>. []
+- Name <one>the two major pathways</one> <two>for repairing double-strand breaks</two>. A: (1) <one>homologous recombination</one> (2) <two<non-homologous end joining</two> []
+- <one>Base-pair additions and deletions</one> <two>within the coding regions of genes</two> <three>are collectively referred to as ... </three>? <one>Frameshift mutations</one>. URL: https://en.wikipedia.org/wiki/Frameshift_mutation []
+- In <one>homologous recombination</one>: <two>information stored in another DNA molecule is required</two>. <three>This other DNA molecule is usually ... </three>? the <one>sister chromatid</one>. []
+- <one>Which person</one> <two>discovered in the year 1927</two> that <three>X rays induced mutations in Drosophila</three>? <one>Hermann Joseph Muller</one>. URL: https://en.wikipedia.org/wiki/Hermann_Joseph_Muller#Discovery_of_X-ray_mutagenesis []
+- Can <one>NER</one> (<two>Nucleotide excision repair</two>) <three>repair interstrand crosslink lesions</three>? <one>Yes</one>. []
+- <one>When</one> is <two>mismatch repair</two> active? Only <one>during the process of DNA replication</one>. []
+- Name <one>a class of agents that can act as mutagens</one> and <two>induces frameshift mutations</two>. A: The <one>acridine dyes</one>. URL: https://en.wikipedia.org/wiki/Acridine []
+- <one>Which enzyme</one> <two>can repair pyrimidine dimers</two>? <one>Photolyase</one>. []
+- Does <one>BRCA2</one> <two>bind preferentially</two> <three>ssDNA</three> or <three>dsDNA</three>? <one>ssDNA</one>. []
+- <one>Non-homologous end joining</one> <two>is usually usd in which cell cycle phase</two>? <one>G1</one>. []
+- Are <one>translesion DNA polymerases</one> <two>error-prone</two>? <one>Yes</one>. URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3783050/ []
+- In a given eukaryotic cell: are <one>depurination events</one> or <one>depyrimidination events</one> more common? <one>Depurination events</one> <two>are much more common</two> than <three>Depyrimidination events</three>. []
+- <one>How many different base substitutions</one> <two>can occur in DNA</two>? <one>12</one> (<two>twelve</two>). []
+- <one>Missense mutations</one> can be of <two>which two types</two>? (1) <one>conservative</one> (2) <one>non-conservative</one> []
+- Does the human tumor suppressor protein <one>BRCA2</one> <two>play a key role in recombinational DNA repair</two>? <one>Yes</one>. []
+- <one>How many</one> <two>endogenous lesions</two> <three>affect a human cell per day</three>? About <one>30_000</one>. []
+- A single full-length <one>BRCA2 protein</one> <two>can bind at the least how many RAD51 monomers</two>? <one>Six</one>. []
+- <one>Bloom's syndrome individuals</one> <two>show a defect in ... </two>? <one>homologous recombination</one>. URL: https://en.wikipedia.org/wiki/Bloom_syndrome []
+- Can <one>DNA-repair systems</one> <two>introduce mutations</two>? <one>Yes</one>. []
+- Can the cell <one>repair apurinic sites</one>? <one>Yes</one>. []
+- Give <one>a specific example for</one> <two>a translesion DNA polymerase</two>. A: Polymerase η, aka <one>Polymerase eta</one>. []
+- If in doubt, <one>which DNA strand is correct</one>? The <one>parental strand</one>. []
+- <one>Base substitutions</one> <two>can be divided into which two subtypes</two>? (1) <one>transitions</one> (2) <one>transversions</one> []
+- Are <one>insertions</one> <two>considered to be point mutations</two>? <one>Yes</one>. []
+- Reichert sich <one>Cohesin</one> an <two>Stellen von Doppelstrangbrüchen</two> an? <one>Ja</one>. []
+- <one>Vergleiche DNA-Schäden</one>: auf 1000 Einzelstrangbrüche kommen wieviele Doppelstrangbrüche? A: Etwa <one>40</one>. []
+- Can <one>RAD51</one> <two>bind to both</two> <three>ssDNA</three> and <three>dsDNA</three>? <one>Yes</one>. []
+- Give another name for <one>virtually error-free DNA repair</one>. A: <one>Accurate DNA repair</one>. []
+- Is <one>homologous recombination</one> <two>fast</two>? <one>No</one>, it is slow. []
+- A <one>mutation</one> that changes a wild-type allele of a gene to a different allele is called ... ? a <one>forward mutation</one>. []
+- Can <one>DNA replication errors</one> <two>lead to indel mutations</two>? <one>Yes</one>. []
+- What happens in a <one>missense mutation</one>? The codon for one amino acid is changed into a codon for another amino acid. []
+- Do <one>synonymous substitutions</one> <two>alter the amino acid sequence of the polypeptide chain</two>? <one>No</one>, never. []
+- The <one>Nobel Prize for DNA repair</one> <two>was given in which year</two>? <one>2015</one>. []
+- Give another name for <one>synonymous mutation</one>. A: <one>Silent mutation</one>. []
+- Possibly <one>the most famous disease caused by a defect in DNA repair</one>, <two>in humans</two>, is ... ? <one>Xeroderma pigmentosum</one>. []
+- <one>Welche Enzyme</one> führen die <two>BER</two> (<two>Base Excision Repair</two>) durch? Die <one>DNA-Glycosylasen</one>. URL: https://en.wikipedia.org/wiki/DNA_glycosylase []
+- Is <one>a single, unrepaired double-stranded break</one> <two>sufficient to kill a cell</two>? <one>Yes</one>. []
+- <one>Welche Reparatur ist umfassender</one>: die <two>Base Excision Repair</two> oder die <two>Nucleotide excision repair</two> (NER)? <one>NER</one>, da hier ein längeres Stück an DNA entfernt wird. []
+- Does <one>mitochondrial DNA</one> <two>mutate more often</two> <three>than DNA stored in the nucleus</three>? <one>Yes</one>. []
+- The <one>deamination of cytosine</one> yields ... ? <one>Uracil</one>. URL: https://en.wikipedia.org/wiki/Deamination#Cytosine

data/lib/studium/exam_topics/dna_replication

@@ -0,0 +1,80 @@
+# =========================================================================== #
+# === DNA Replication
+#
+# Everything about DNA replication, be it in eukaryotes or prokaryotes.
+# =========================================================================== #
+
+- Errors during DNA replication introduce ... ? <one>mutations</one>.
+- Why is the single-strand binding protein required during DNA replication? These proteins prevent the re-annealing of the two DNA strands.
+- The <one>enzyme DNA helicase</one> requires energy in the form of ... ? <one>ATP</one>.
+- During DNA replication, where could DNA gyrase typically be found? It could be found ahead of replication fork, where it inserts negative supercoils, in order to counteract the positive supercoils tha are created due to the unwinding of DNA.
+- Okazaki fragments can be found where? On the lagging strand, during DNA replication.
+- Is there a DNA polymerase known that can initiate a new DNA chain? <one>No</one>. They all need a primer.
+- Die <one>DNA Polymerase I</one> <two>in Escherichia coli</two>: <three>wo</three> kann deren <four>5'-3'Exonuclease Funktion</four> gefunden werden? Im <one>aminoterminalen Bereich</one>.
+- Die <one>DNA-Polymerase I</one> in Escherichia coli kann DNA polymerisieren. Wo in diesem Enzym findet sich diese Funktion? Im C-terminalen Bereich (also im carboxyterminalen Bereich).
+- <one>DNA-Replikation</one> hat vor allem mit welchen Stellen ein Problem? Mit Wiederholungssequenzen, also <one>repeats</one>.
+- Does <one>RAD51</one> have a ATPase activity? Yes.
+- Is end-joining error-prone? <one>Yes</one>.
+- If a cell is going to repair UV damage to DNA, it will typically make use of ... which pathway? <one>Nucleotide excision repair</one>.
+- Name a nucleoside analog that blocks DNA replication. A: <one>Gemcitabine</one>. 
+- Ein <one>Replikationsauge</one> entsteht am ... ? <one>Replikationsursprung</one>.
+- Für die <one>DNA Replikation in Bakterien</one> sind vor allem welche Proteine extrem wichtig? <one>DNA-Polymerasen</one>.
+- <one>DiaA</one>, important for DNA replication in bacteria, consists of how many individual subunits? It ias a homotetramer - thus, it requires four subunits.
+- Domain I of the DnaA protein is also called ... ? Helicase interaction.
+- Which part of the DnaA protein binds DNA? <one>Domain IV</one>.
+- DnaA has how many different domains? <one>Four</one>.
+- How does the level of ATP-DnaA change during the cell cycle? It will steadily increases during the cell cycle.
+- <one>DnaA</one> is the DNA synthesis ... A: initiator.
+- A <one>DNA-unwinding element</one> may have which important property? It is AT-rich, thus facilitating being more readily opened up during DNA-replication.
+- The AT-rich 13mer regions in oriC, such as in the E. coli genome, are also alternatively called ... ? <one>DNA unwinding element</one>.
+- Name a famous disease that represents a paradigm of a DNA repair disorder with a clear pathological link between genotype and phenotype. A: <one>Xeroderma pigmentosum</one>. URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3504433/
+- Für die <one>Initiation der DNA-Replikation in Bakterien</one> ist im <two>DnaA-Protein</two> <three>welche Aminosäure am wichtigsten</three>? <one>Arg399</one>, also <two>Arginin</two>.
+- Name <one>two enzymes</one>, at the least in bacteria, that travel along the DNA ahead of the "replication fork". A: (1) "DNA-Helicase" (2) <one>DNA-Gyrase</one>
+- Name <one>two factors</one> that are important for prokaryotes to control the initiation of DNA-Replication. A: (1) <one>methylation of DNA at the origin</one> (2) <one>attachment to the cell membrane</one>
+- Die <one>Synthesephase der DNA-Replikation</one> wird wie genannt? <one>Elongation</one>.
+- <one>In Eukaryoten</one>: wird im Zuge der DNA-Replikation zuerst das Heterochromatin repliziert? Nein - zuerst repliziert das Euchromatin, dann das <two>Heterochromatin</two>.
+- Das berühmte <one>Meselson-Stahl-Experiment</one> von <two>Matthew Meselson</two> und <two>Franklin Stahl</two> aus dem Jahre <three>1958</three> verwendete welches Bakterium? <one>Escherichia coli</one>.
+- Ter-site in Bacteria: ter stands for ... ? <one>Terminus of replication</one>.
+- In Pol III, which component performs the <one>proofreading-activity</one>? <one>DnaQ</one>. URL: https://en.wikipedia.org/wiki/DnaQ
+- Was ist ein wichtiger Unterschied zwischen <one>rolling circle Replikation</one> und "Theta-Replikation"? (1) <one>rolling circle replication</one>: <two>unidirektionale Replikation</two> (2) <one>theta replication</one>:          <two>bidirektionale Replikation</two>
+- Wann wurden die ersten <one>DNA-Helikasen</one> entdeckt? <one>1976</one>, durch Hoffmann-Berling.
+- Aside from DNA, the protein DnaA can also bind to ... ? <orange>ATP</orange>.
+- <one>DnaA</one> depends a lot on which other cellular molecule? On <one>ATP</one>. URL: https://en.wikipedia.org/wiki/DnaA
+- Kommt es beim <one>non-homologous end-joining</one> zu einem <three>Doppelstrangbruch in der DNA</three>? Ja. URL: https://en.wikipedia.org/wiki/Non-homologous_end_joining
+- The primers used for DNA replication in Bacteria: are these <one>RNA-Primer</one> or <one>DNA-Primer</one>? They are <one>RNA-Primer</one>.
+- Name a protein that can inhibit DNA replication in Bacteria. A: <one>SeqA</one>.
+- <one>Which enzyme</one> <two>synthesizes the Okazaki fragments</two>? The <one>DNA Polymerase III</one>.
+- Bei der DNA-Replikation in Bakterien gibt es ein Protein das RIDA genannt wird. Was heisst <one>RIDA</one>? <one>Regulatory inactivation of DnaA</one>.
+- In <one>E. coli</one>: which protein <two>initiates DNA replication</two>? The <one>DnaA-Protein</one>.
+- Wer entfernt den Beta-Ring von der DNA? Der <one>Gamma-Komplex</one>.
+- <one>Primer</one> bei der DNA-Synthese müssen unbedingt welche Eigenschaft besitzen? Sie müssen 3'OH Enden vorweisen.
+- What is the precise role that the <one>DnaC-Protein</one> plays during DNA Replication? The <one>DnaC-Protein</one> is a <two>loading factor</two>. It <three>loads DnaB onto the DNA strand at the origin</three>. URL: https://en.wikipedia.org/wiki/DnaC
+- <one>Welches Molekül</one> synthetisiert den Primer bei der eukaryoten DNA Replikation? Die <one>Primase im Primosom</one>.
+- Nenne zwei Kennzeichen <one>prokaryoter origins of replication</one>. A: (1) sie besitzen "dna-A Boxen" (2) sie <one>sind AT-reich</one>
+- Bei der Regulation der DNA-Replikation in Bakterien gibt es das wichtige Protein <one>DiaA</one>. Wieviele Untereinheiten hat es? Dia ist ein Homotetramer - besitzt somit 4 Untereinheiten.
+- How is the <one>AT-rich region</one> in <three>oriC</three> called? This is the <lightgreen>DNA-unwinding element</lightgreen>.
+- Give another term for the <one>DNA-replication process machinery</one>. A: The <one>replisome</one>. URL: https://en.wikipedia.org/wiki/Replisome
+- Ist die DNA-Reparatur in Eukaryoten an die Transkription gekoppelt? Üblicherweise ja.
+- Wie lange ist der <one>oriC in Bakterien</one>, zumindest in E. coli, in bp? Etwa <one>250bp</one>. URL: https://en.wikipedia.org/wiki/Origin_of_replication#Prokaryotic
+- Which protein arrests the <one>DnaB helicase</one> at <three>Ter site</three>, thus "blocking replication forks"? The site-specific DNA binding protein <one>Tus</one> (<two>Terminus utilization substance</two>) does this.
+- In bacteria, let's assume that we have proteins such as <one>DnaA</one>, DnaB, DnaC ... down to DnaZ. Given the <orange>primosome</orange> in bacteria, which two Dna-proteins are part of the primosome? (1) <one>DnaB</one> (2) <one>DnaG</one>
+- The zone of unwound DNA where replication occurs is known as ... ? The <one>replication fork</one>; at the least in Bacteria. URL: replication fork
+- In E. coli: wieviele verschiedene DNA-Polymerasen beschäftigen sich mit <one>beschädigter DNA</one>? <one>3</one>.
+- <one>Typ ... Topoisomerasen</one> werden für die Termination ringfömiger Chromosomen benötigt. A: <one>Typ II Topoisomerasen</one>.
+- In <one>E. coli</one>: <two>wo beginnt die Replikation des Genoms</two>? Am <one>oriC</one> Bereich. URL: https://en.wikipedia.org/wiki/Origin_of_replication
+- During <one>bacterial conjugation</one>: <two>which endonucleases</two> is required to initiate the rolling circle replication? The <one>Tra1 Endonuclease</one>. URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC134963/
+- <one>Replication within a plasmid</one> begins at ... ? At an <one>origin of replication</one>. URL: https://en.wikipedia.org/wiki/Origin_of_replication
+- <orange>DnaA-ATP</orange> kann in <one>DnaA-ADP</one> konvertiert werden. Für eine effiziente Konversion benötigen wir welch weiteres Protein hierzu? Die "sliding clamp".
+- A typical <one>eukaryotic replicon</one> ranges from-to? 20.000 to 300.000 bp.
+- In Bakterien bei den minE Mutanten, welches Problem haben diese Bakterien und wieso? Der "Z-Ring" wird nicht gebildet; dadurch entstehen "filamentöse Zellen".
+- Is the "DiaA protein" good or bad for DNA replication? The DiaA Protein "stimulates DNA replication".
+- "DNA-polymerases" are not only important for DNA replication, but also at which other cellular function? "DNA-repair" (of damaged DNA).
+- Die "DNA-Polymerase I", aus E. coli, besteht aus n Aminosäuren? "928". URL: https://en.wikipedia.org/wiki/DNA_polymerase_I
+- Nenne zwei Bedingungen, die erfüllt sein müssen, damit die DNA Polymerase I in E. coli, in-vitro, DNA erfolgreich replizieren kann. A: (1) Die Gegenwart von "dNTPs" (2) "Matrizen-DNA"
+- What role does "Dia" play in DNA-Replication of Bacteria? DiaA stimulates DNA replication and specifically binds to domains I and II at the N-terminus of the DnaA protein. The DiaA tetramer can bind multiple molecules of DnaA, and thus can serve as a bridge to bring two DnaA molecules together. Binding of DnaA to the DiaA tetramer may serve as a mechanism to overcome the effects of random diffusion and facilitate inter-DnaA interactions.
+- Die Primase erstellt den RNA-Primer für die DNA-Replikation. Wie lange sind diese Primer-Stücke? Etwa 10-12 Nukleotide.
+- What is the role of "Hda" during DNA-Replication in Bacteria? Hda ("homologous to DnaA") stimulates the ATPase activity of DnaA assembled at oriC B. The ATP-Hydrolysis then leads to the disassembly of the DnaA superhelix.
+- In the "rolling-circle model" of DNA-replication, which DNA end is progressively displaced? The 5-prime end.
+- In DNA Replication, the hydrolysis of DnaA-ATP is crucial to the regulation of initiation. By which mechanism does this occur? By a replication-coupled feedback mechanism called "RIDA" (regulatory inactivation of DnaA).
+- Name a replication model without replication bubble. A: The rolling-circle model.
+- Name the two replicative DNA Polymerases of Eukaryotes. A: (1) "Alpha" (2) "Delta"

data/lib/studium/exam_topics/ecogenetics

@@ -0,0 +1,26 @@
+# =========================================================================== #
+# === ECOGENETICS
+#
+# ökogenetik tag. Öko tag. Auch Lebensgemeinschaften der Mikroorganismen.
+# ECOGENETICS tag. Ökogen tag. Ecogen tag. Ökogentag.
+# Ökogen tag. Ökogen tag. ÖKOGENETIK Tag.
+# =========================================================================== #
+
+- On average: do <one>bacteria</one> or <one>archaea</one> have <two>larger genomes</two>? <one>Archaea</one> <two>have larger genomes</two>.
+- Was ist unterhalb der <one>euphotischen Zone</one>? Die <one>aphotische Zone</one>. URL: https://en.wikipedia.org/wiki/Aphotic_zone
+- Ist meistens die allelische Vielfalt oder die genotypische Vielfalt höher? Die genotypische Vielfalt.
+- Give another term for <one>retroderived elements</one>? <one>Retrotranscripts</one>.
+- Why is <one>5-methylcytosine</one> considered a "hot spot"? Because it can <one>spontaneously deaminate</one> to <two>thymine</two>.
+- Im Jahre 2000 wurde <one>SIP</one> eingeführt in der mikrobiellen Ökologie. Was heisst <one>SIP</one>? <one>Stable-isotope probing</one>. URL: URL: https://en.wikipedia.org/wiki/Stable-isotope_probing
+- Are Transitions or Transversions more abundant? Transitions are 20X more abundant than transversions.
+- Deamination of 5-methylcytosine leads to ...? Thymine.
+- Why is the endosymbiont <one>Buchnera aphidicola</one> so important for aphids? Aphids feed on plant sap, sucking it out of the phloem. This is a diet poor in amino acids, and aphids can not synthesize 10 of the 20 default amino acids. But their endosymbiont helps them, supplying them with these amino acids. This is an example for a 150 to 250 Mio years old symbiotic relationship.
+- What means "pan genome" in Ecogenetics? <one>Core</one> genome.
+- What is the <one>great plate count anomaly</one>? This means that plate counts of cells obtained by cultivation are usually much lower than than those obtained from direct counting via microscope.
+- Azotobacter is what kind of organism? It is a nitrogen-fixing bacterium.
+- Revertants can be of which 2 types? (1) same-site revertants (2) true revertants
+- How many viruses exist on planet earth? 10 ** 31 viruses are estimated to exist on earth.
+- What are "ecotypes"? These are genetic lineages with ecologically relevant physiological differences.
+- Who are the smallest known photosynthetic organism? The marine cyanobacteria from the Prochlorococcus genus.
+- Wie lebt "Richelia"? Intrazellulär.
+- Viruses may be important in ecology. List 3 reasons why. A: (1) nutrient cycling (2) horizontal gene transfer (3) microbial biodiversity

data/lib/studium/exam_topics/ecological_agriculture

@@ -0,0 +1,12 @@
+# =========================================================================== #
+# === Ökologischer Landbau
+#
+# Inkludiert auch Grünlandbewirtschaftung.
+# =========================================================================== #
+
+- Wenn wir eine Karten sehen mit <one>Grünland FEUCHT</one>, was können wir daraus schliessen? Das auf diesen Wiesen und Weiden mit hoher Wahrscheinlichkeit keine Trockenheit auftreten wird.
+- Nenne mindestens 3 Ausgangsmaterialien für Humus. A: (1) Ernterückstände (2) Wurzelrückstände (3) Stroh (4) Gründüngung 
+- Was meinen wir mit "Grünland"? Als Grünland werden landwirtschaftlich genutzte Flächen bezeichnet, auf denen "Gras und krautige Pflanzen" als Dauerkultur wachsen.
+- Was mag mit den nicht mehr genutzten Grünlandflächen in den Almregionen geschehen? Diese könnten langfristig zu Wald werden.
+- Wie wirken sich sehr häufige Regentage auf die qualitative Futterkonservierung aus? Sie wirken sich negativ aus.
+- In der Grünlandbewirtschaftung sollten wir "Futterverschmutzung" vermeiden. Hierbei gibt es vor allem 3 Punkte bei der Nutzung eines Grünlandfeldes. Welche? (1) Die "Schnitthöhe von mindestens 5cm" sollte eingehalten werden (2) Die "Mäh-, Werbe- und Erntegeräte" sollten sorgfältig eingestellt und kontrolliert werden (3) Es sollten nur möglichst gut abgetrocknete Bestände gemäht werden