studium 0.18.7

data/lib/studium/exam_topics/pcr

@@ -0,0 +1,155 @@
+# =========================================================================== #
+# === PCR tag
+#
+# Seit Dezember 2013 hat die PCR eine eigene Rubrik.
+# =========================================================================== #
+
+- The most commonly employed temperature in order to heat up and melt dsDNA for PCR is ... n °C? About <one>95° C</one>.
+- As <one>PCR</one> reaches later cycles, it enters the ... phase. A: <one>plateau</one> phase.
+- Name <one>the 5 components in a typical PCR mix</one>. A: (1) the template DNA (2) buffer (3) dNTPs (4) primers (5) <one>polymerase</one>
+- What was essentially the critical development that led up to the universal adoption of the PCR technique? The concept of using the thermal stable DNA polymerase that could tolerate the high temperature of the repeated denaturation steps.
+- The primers used in a PCR should typically be n nucleotides long (from-to)? About 17-25 nucleotides.
+- <one>Error-prone PCR</one> often uses which enzyme? The <one>Taq DNA polymerase</one>.
+- In regards to the primers used in a PCR: which word could we use to describe the two primers, owing to a military term? <one>Flanking oligonucleotide primers</one>.
+- <one>Hybridization PCR</one> uses how many probes? <one>Two</one>.
+- Why can we say that <one>Hybridization PCR</one> is superior to TaqMan PCR in special cases? Because differences between variants of a gene can be detected with it.
+- In a PCR: why is there a step to increase the temperature to ~ 95°C? This is the heating step; in this step the DNA double strands are separated (denatured) into two complementary single strands. This is necessary because the primers have to bind to the corresponding single stranded DNA.
+- The <one>activation temperature of the Taq polymerase</one> is between n°C and n°C? Between <one>70°C and 80°C</one>.
+- How many <one>starting molecules</one> are required in a PCR? Two. The <one>forward primer</one> and the <one>reverse primer</one>.
+- According to MIQE, the acronym <one>'qPCR'</one> describes ... ? <one>quantitative real-­time PCR</one>.
+- <one>RT-­PCR</one> is the name for ... ? <one>Reverse transcription PCR</one>.
+- <one>Gene splicing</one> can be <two>achieved by which type of PCR</two>? By <one> overlap extension polymerase chain reaction</one>.
+- <one>Warum</one> wird die PCR nach mehreren Zyklen immer langsamer? Meistens <one>da einer der Reaktionsbestandteile (Primer, dNTPs oder die Polymeraseaktivität) aufgebraucht werden</one>. Dies verlangsamt die Produktbildung bis diese schließlich zum Erliegen kommt.
+- What are <one>vectorettes</one>? <one>Vectorettes</one> enable PCR amplification of DNA sequences which lie between a single known primer and a nearby restriction site.
+- <one>Which PCR</one> can be used in order to delete central parts of a protein coding sequence? The <one>template switching PCR</one>. URL: https://www.wikiwand.com/en/Template_switching_polymerase_chain_reaction
+- Nenne ein Beispiel für eine <one>high-fidelity DNA polymerase</one>. A: Die <one>Pfu-DNA-Polymerase</one>. URL: https://en.wikipedia.org/wiki/Pfu_DNA_polymerase
+- <one>SYBR Green I</one> intercalates <two>where</two> exactly (in general)? Into <one>dsDNA</one>.
+- In einer typischen PCR: <one>wieviele Zyklen (von-bis) werden hierbei durchlaufen</one>? <one>25-35</one>.
+- In a PCR: how is the variant called where <one>only one primer is used</one>? <one>Asymmetric PCR</one>.
+- Name <one>three ways</one> how to increase the error-rate of Taq DNA Polymerase in error-prone PCR. A: (1) add Mn 2⁺ (2) increase the concentration of Mg 2⁺ (3) <one>add unequal amounts of the 4 deoxynucleoside triphosphates to the reaction buffer</one>
+- Nenne <one>die 3 Temperaturen</one> in einer typischen PCR. A: (1) <one>94°C</one> (2) <one>54°C</one> (3) <one>72°C</one>
+- Wofür steht die Abkürzung bei der <one>CHART-PCR</one>? <one>Chromatin accessibility real-time PCR</one>. URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3617569/
+- Bei der Realtime PCR: was heisst <one>Ct-Wert</one>? <one>Cycle threshold</one>.
+- Name a procedure in which we may employ <one>reassembly PCR</one>. A: In <one>DNA shuffling procedure</one>.
+- We require <one>bivalent cations</one> for a PCR, usually <two>Mg²⁺</two> but we can also use <two>Mn²⁺</two>. When may we wish to use very high concentrations of Mn²⁺? When we <one>wish to increase the error rate during DNA synthesis</one>.
+- In <one>error-prone PCR</one> we <two>wish to create mutations</two>. Aside from using different divalents (ions), name another simple way how to achieve this. A: We will <one>use conditions that allow the addition of wrong nucleotides</one>, by using different quantities of dNTPs.
+- Welchen <one>Farbstoff</one> verwenden wir bei der <one>real-time PCR (RT-PCR)</one>? <one>SYBR Green I</one>. URL: https://en.wikipedia.org/wiki/SYBR_Green_I
+- <one>ddPCR</one> stands for ... ? <one>Droplet Digital PCR</one>. URL: https://en.wikipedia.org/wiki/Digital_polymerase_chain_reaction
+- Wieso kann die <one>RT-PCR</one> nur <two>mRNA</two> amplifizieren? Wir verwenden ja nur oligo(dT)-Primer, die an die 3' PolyA mRNA binden können.
+- Warum mag es nicht immer sinnvoll sein eine <one>realtime-PCR</one> einzusetzen? Eine realtime-PCR mag nicht immer gut sein, da eine Genfamilie die Analyse erschweren kann ("single-copy gene").
+- The <one>annealing temperature</one> for a PCR is in what relation to the Tm melting temperature? Approximately 4°C below the Tm.
+- The <one>Droplet Digital PCR</one> uses what exactly for its droplet system? A <one>water-oil emulsion</one>. 
+- Der <one>Schmelzpunkt der PCR</one> sollte zwischen ... liegen? Zwischen 55°C und <one>65°C</one>.
+- Nenne eine sehr einfache Methode, <one>die Genauigkeit der PCR</one> zu erhöhen. A: Wir <one>erhöhen</one> einfach <two>die Annealingtemperatur</two>.
+- Wie geht die <one>PCR-Zyklus Formel</one>, <two>zur Berechnung der Zyklen</two>? <one>2 ** n</one>, wobei <two>n die Anzahl an Zyklen bezeichnet</two>.
+- What is <one>the half-life of Taq-Polymerase at 95°C</one>? About <one>40 minutes</one>.
+- <one>Directed Evolution</one> ist oft mit welcher PCR verknüpft? <one>Error-prone PCR</one>. URL: https://sites.ffclrp.usp.br/pbbg/english/topics/molecular_biology/error-prone_pcr.htm
+- What is the key idea behind <one>hot start PCR</one>? Prevent Taq-polymerase activity at low temperature during setup and initial annealing stage.
+- Wir können zwischen zweistufiger und dreistufiger PCR unterscheiden. Welcher Schritt ist bei beiden PCRs vorhanden? <one>Der 1. Schritt</one>: <two>Denaturierung der DNA</two>.
+- Die <one>Tth Polymerase</one> für die PCR unterscheidet sich von den anderen PCR-Polymerasen wodurch? Sie hat eine <one>starke reverse Transkriptase Aktivität</one>.
+- The <one>differential display PCR</one>: <two>why</two> is it used? It is used to <one>specifically amplify mRNA from eukaryotic cells</one>.
+- Name <one>a restriction endonuclease</one> that is used in <two>mePCR</two> (<two>Methyl PCR</two>). A: <one>DpnI</one>, which cuts only <two>methylated GATCs</two>.
+- In <one>realtime PCR</one>: <two>when</two> do we measure the level of fluorescence? At the end of each elongation phase.
+- In <one>error-prone PCR</one> we wish to avoid ... ? <one>Proofreading</one>, because <two>we seek to generate new variants</two>.
+- <one>Temperatur</one> bei der PCR-Elongation - und warum diese Temperatur? <one>72 Grad Celsius</one>, dem <two>Temperaturoptimum der Taq-DNA-Polymerase</two>.
+- <one>Wann</one> wurde die PCR erfunden? <one>1983</one>. URL: https://en.wikipedia.org/wiki/Polymerase_chain_reaction
+- Was ist <one>das entscheidende Prinzip der PCR</one>? Das <one>Wiederholen der einzelnen Reaktionsschritte</one>.
+- Was ist die <one>Grundüberlegung</one> hinter einer <two>zweistufigen PCR</two>? Wir wollen uns hierdurch Zeit ersparen.
+- <one>Emulsion PCR</one> takes place in ... ? <one>microreactors</one>. URL: https://en.wikipedia.org/wiki/Massive_parallel_sequencing#Emulsion_PCR
+- <one>A single PCR cycle</one> takes about ... ? <one>5 minutes</one>.
+- <one>Stoffel-Fragment</one> versus <one>Taq-Polymerase</one>: <two>welche der beiden ist hitzestabiler</two>? Das <one>Stoffel-Fragment</one>.
+- Name one <one>big limitation of the PCR</one>. A: We <one>need to have the sequence information available</one>, because it is necessary for desinging proper primers to the target sequence.
+- <one>A-T cloning</one> adds what where to? It <one>adds an extra A</one> to the 3' end of the PCR product.
+- Name a curious way <one>how to inhibit PCR</one>. A: Wooden toothpicks made of birch.
+- Nenne zwei <one>nichtradioaktive Markierungen</one> die wir bei der PCR einsetzen können. A: (1) <one>Biotinmarkierung</one> des 5' Ende (2) <one>Fluoreszenzmarkierung</one>
+- Nenne ein <one>fluoreszierendes Molekül</one>, das in der Real-Time PCR verwendet wird. A: <one>SYBR Green I</one>. URL: https://en.wikipedia.org/wiki/SYBR_Green_I
+- <one>Welche Primer</one> werden meistens bei der <two>RACE PCR</two> verwendet? <one>Degenerate Primer</one>.
+- What is <one>the minimum time</one> required for <two>denaturation</two> in a <three>rapid-cycle PCR</three>? Less than one second.
+- Why is <one>the GC-content of PCR Primers</one> recommended to be at 50%? Because the primer must bind tightly to its target sequence and this is only possibly if the binding is tight.
+- <one>Was für eine Polymerase</one> kommt in der PCR überlicherweise zum Einsatz? Eine <one>thermostabile PCR</one>.
+- Wofür steht die Abkürzung <one>MS-PCR</one>? <one>Methylation sensitive PCR</one>.
+- Can <one>real-time PCR</one> be used for <two>whole transcriptome analysis</two>? <one>No</one>.
+- Why do we denature <one>long PCR</one> only for two seconds? To protect the Purin Bases.
+- Gib eine grobe Abschätzung der <one>Annealingtemperatur</one> während einer PCR an, also eine einfache Formel. A: <one>Tm = 4 * (G + C) + 2 * (A + T)</one>.
+- Andere Bezeichnung für eine <one>quantitative PCR</one>? <one>Real-time PCR</one>. URL: https://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction
+- The <one>Emulsion PCR</one> uses what <two>kind</two> of beads? <one>DNA capture beads</one>.
+- What does <one>IPCR</one> stand for? <one>immuno-PCR</one>.
+- Die <one>PCR</one> besteht aus D,A,E. Nenne diese Schritte. <two>Bei welcher Temperatur finden diese jeweils statt</two>? (1) <one>Denaturation</one>: <two>94°C</two> (2) <one>Annealing</one>:    <two>60°C</two> (3) <one>Extension</one>:    <two>70°C</two>
+- Name one <one>limitation of the PCR technique</one>. A: The <one>target DNA-sequence for primer-binding must be known</one>.
+- Via PCR: how could we delete the central parts of a protein? We could use the <one>template switching PCR</one>. URL: https://en.wikipedia.org/wiki/Template-switching_polymerase_chain_reaction
+- <one>Which PCR variant</one> employs a <two>hot start</two>? The <one>Multiplex PCR</one>.
+- Nenne <one>zwei Substanzen</one>, die die Spezifität einer PCR verbessern können. A: (1) <one>Formamid</one> (2) <one>DMSO</one>
+- Hemmt <one>Pyrophosphat</one> die Polymerase? Ja; <one>zumindest in hoher Konzentration</one>.
+- What does the abbreviation <one>spPCR</one> stand for? <one>splinkerette PCR</one>.
+- <one>Wie lange</one> dauert ein <two>PCR-Reaktionszyklus</two> (von-bis)? <one>5-10 Minuten</one>.
+- What is the <one>target sequence</one> in a PCR? This is <one>the sequence that will be amplified during the course of a PCR reaction</two>.
+- Was ist eine <one>GC-Klammer</one> und wieso verwenden wir sie? Die <one>GC-Klammer</one> wird in der PCR beim <two>Primer Design</two> verwendet. Es ist eine Sequenzfolge mit G und C, vor allem in den letzten fünf Basen eines Primers. Dies erhöht die Spezifität der Primerbindung. Ein Primer sollte etwa 50% GC-Anteil haben.
+- In <one>enzyme engineering</one>, for the DNA shuffling procedure, we may make use of a specific PCR during that procedure. <two>What is the name of this PCR</two>? <one>Reassembly PCR</one>.
+- Nenne ein konkretes Einsatzgebiet für das <one>Stoffel-Fragment</one>. A: <one>DNA-Sekundärstrukturen</one>.
+- <one>Welche Variante der PCR</one> teilt eine Probe in 20000 Tröpfchen ein? Die <one>digital droplet PCR</one>.
+- Why is the <one>template switching PCR</one> useful? It allows use to remove functional domains from a protein.
+- Why the name <one>gradient PCR</one>? Because we make use of a "temperature gradient" of the annealing temperature. This can be used to find the optimum for a given PCR reaction.
+- How do we call <one>the two different primers</one> used in a PCR? (1) <one>forward primer</one> (2) <one>reverse primer</one>
+- <one>Which PCR</one> uses a lot of primers? The <one>multiplex PCR</one>, which was first described in <two>1988</two>. URL: https://en.wikipedia.org/wiki/Multiplex_polymerase_chain_reaction
+- <one>Wann</one> sollte die <two>qPCR</two> beendet werden? Noch während der <one>exponentiellen Amplifikationsphase</one>.
+- What is <one>the default dye</one> that is used in a standard <two>real time PCR</two>? <one>SYBR Green I</one>. URL: https://en.wikipedia.org/wiki/SYBR_Green_I
+- <one>Welche PCR</one> kann Verunreinigungen vermeiden? Die <one>UNG-PCR</one>.
+- Die Abkürzung <one>ddPCR</one> steht für ...? <one>droplet-digital-PCR</one>. URL: https://en.wikipedia.org/wiki/Digital_polymerase_chain_reaction#Droplet_Digital_PCR
+- What is a <one>multiplex PCR</one>? The <one>multiplex polymerase chain reaction</one> refers to the use of polymerase chain reaction to amplify several different DNA sequences simultaneously.
+- Bei der PCR: wie untscheidet sich die <one>Vent-Polymerase</one> von der <one>DeepVent-Polymerase</one>? DeepVent ist <one>viel stabiler</one> bei höherer Temperatur. Es ist überhaupt die stabilste Polymerase bei hohen Temperaturen.
+- Wie funktioniert eine <one>nested PCR</one>? Bei einer <one>nested PCR</one> werden die Amplifikate aus der ersten PCR selbst als Template eingesetzt.
+- Wie lange sollte ein <one>Primer</one> für die PCR sein (von-bis)? <one>20 bp - 30 bp</one>.
+- <one>Why</one> does the <two>long PCR</two> use two different PCR-Polymerases? Because the 2nd polymerase, usually <one>Pfu polymerase</one>, possess proofreading activity.
+- <one>PCR reactions</one> can amplify up to n bp of DNA? Fragments up to <one>40 kbp</one> in size.
+- In der PCR: was heisst <one>SOE-PCR</one>? <one>Splicing by overlap extension</one>.
+- Was erreicht man dank der <one>Multiplex-PCR</one>? Man vervielfacht innerhalb eines Ansatzes mehrere Fragmente.
+- Bei manchen PCRs wird die <one>Tth DNA-Polymerase</one> eingesetzt. Wofür steht die Abkürzung <two>Tth</two>? <one>Thermus thermophilus</one>.
+- Bei der <one>Realtime PCR</one>: was besagt der <two>Ct-Wert</two>? Er beschreibt den Teil der Kurve, in dem die Fluoreszenz erstmals exponentiell über den Hintergrundwert ansteigt.
+- <one>Why</one> is a very high concentration of free primers in a PCR mix not good to have? Because it may favor <one>unspecific annealing</one>.
+- <one>Welcher Farbstoff</one> wird bei der <two>Realtime-PCR</two> verwendet? <one>SYBR Green I</one>. URL: https://de.wikipedia.org/wiki/SYBR_Green_I
+- Der <one>forward primer</one> einer PCR korreliert mit ...? Dem <one>Beginn des Gens</one>.
+- <one>Welche Sonde</one> kommt bei der <two>Real-Time PCR</two> üblicherweise zum Einsatz? Eine <one>TaqMan Sonde</one>. URL: https://de.wikipedia.org/wiki/Real_Time_Quantitative_PCR#TaqMan-Sonden_(auch_Hydrolyse-Sonden)
+- Why does <one>long PCR</one> use more than one polymerase? Standard Taq polymerase can not proofread, which is important for longer PCR, so we use Pfu or Tli polymerase.
+- Why is <one>A-T cloning</one> so popular? Because a vector with T overhangs can be used to clone a PCR product without digesting it with restriction enzymes. In other words, we will not need a restriction enzyme.
+- Andere Bezeichnung für eine <one>verschachtelte PCR</one>? <one>Nested PCR</one>. URL: https://en.wikipedia.org/wiki/Nested_polymerase_chain_reaction
+- Andere Bezeichnung für <one>PCR-Geräte</one>? <one>Programmierbare Thermostate</one>.
+- Nenne einen möglichen Nachteil der PCR in der Humanmedizin. A: <one>Falsch negative Ergebnisse</one> können verursacht sein.
+- Nenne eine <one>PCR-hemmende Substanz</one>. A: <one>EDTA</one>. URL: https://de.wikipedia.org/wiki/Ethylendiamintetraessigs%C3%A4ure
+- For amplification of long segments of DNA (up to 35 kb), which polymerase is typically used in PCR? The <one>Tfl polymerase</one>.
+- How do we call the two primers used in PCR? Forward primer and reverse primer.
+- <one>Temperaturoptimum</one> der Taq-Polymerase? 72°C.
+- Das <one>Inverse fusion PCR cloning (IFPC) System</one> umfasst wieviele Schritte? <one>3</one>. URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0035407
+- <one>Bei welcher PCR</one> werden <two>Wachskügelchen</two> verwendet? Bei der <one>hot start</one> PCR.
+- Besitzt das <one>Stoffel-Fragment</one> eine <two>5'→3' Exonukleaseaktivität</two>? Nein.
+- Wieso benötigen wir Mg²⁺-Ionen für die PCR? Mg²+-Ionen bilden einen löslichen Komplex mit Nukleotiden, wodurch das Substrat gebildet wird, welches von der DNA-Polymerase erkannt wird.
+- <one>Primers for use in a PCR</one> should in general not go above a melting temperature of 65°C. Why not? They have a tendency for <one>secondary annealing</one>.
+- In a <one>hot-start PCR</one>: how can it be ensured that the polymerase remains inactive until about 70°C temperature? We employ an antibody here which normally keeps the polymerase inhibited.
+- Does <one>12% sucrose</one> inhibit PCR? No.
+- Besitzt das <one>Stoffel-Fragment</one> eine 3'→5' Exonukleaseaktivität? Nein.
+- Which phase in PCR do we wish to avoid or delay? The <one>plateau phase</one>.
+- In <one>realtime PCR</one>, we need RNA for normalization. Which RNA do we use for that? RNA for housekeeping genes.
+- Why the name <one>T</one>/<one>A cloning of PCR amplified DNA</one>? Because the PCR insert must have an overhanging 3' A, and the mother DNA must have an overhanging 5' T.
+- Was heisst <one>E-PCR</one>? <one>Expression PCR</one>.
+- In <one>PCR</one>, most thermal cyclers have <two>heated lids</two>. Why? To <one>prevent condensation at the top of the reaction tube</one>.
+- Mnemo für PCR um ihre <one>grundlegenden Schritte</one> zu beschreiben? Der <one>DAE Weg</one>. (<two>Denature</two>, <two>Annealing</two>, <two>Elongation</two>).
+- Benötigen wir bei der <one>Gibson Assembly Klonierung</one> die PCR? Ja. URL: https://de.wikipedia.org/wiki/Gibson_Assembly
+- "Droplet Digital PCR" (ddPCR) is a method for performing digital PCR that is based on ... technology. A: <one>Water-oil emulsion droplet technology</one>.
+- <one>Which company</one> bought the PCR technique? <one>Roche</one>. URL: https://en.wikipedia.org/wiki/Roche
+- <one>Wo</one> werden PCRs durchgeführt? In einem <one>Thermocycler</one>. URL: https://de.wikipedia.org/wiki/Thermocycler
+- Nenne <one>drei übliche Komponenten</one> eines <two>PCR-Puffers</two>. A: (1) <one>Mg2⁺</one>-Ionen (2) "Cl-"-Ionen (3) <one>dNTPs</one>
+- Why do we require a longer primer for PCR? <one>Long primers are more specific</one> <two>for binding to the target sequence</two>.
+- Was meinen wir mit einer <one>niedrigen Nachweisgrenze</one> der <two>PCR</two>? Das hier theoretisch bereits <one>ein einziges Templatmolekül ausreicht</one>.
+- Name a solution to <one>pre-PCR mispriming</one>. A: We could use the <one>hot-start PCR</one>.
+- Wieso verwenden wir eigentlich die <one>inverse PCR</one>? Wir können mit ihrer Hilfe in unbekannte Genom-Bereiche vordringen.
+- Warum ist es so wichtig das das Enzym bei der PCR <one>sehr genau arbeitet</one>? Die PCR läuft zyklisch ab. Das heisst das ein fehleranfälliges Enzym zu einer überproportionalen Anhäufung von Mutanten der Zielsequenz führen würde.
+- Was heisst <one>USE-PCR</one>? Unique site elimination PCR.
+- Wie lange sollten <one>typische PCR Primer</one> sein (von-bis)? Etwa <one>18-22 bp</one>.
+- What is the main advantage of a <one>single-primer PCR</one>? No primer-dimer artifacts.
+- Nenne <one>zwei Einschränkungen der PCR</one>. A: (1) die <one>Nukleotidsequenz muss bekannt sein</one> (2) geringste Kontaminationen stellen ein Problem dar
+- <one>PCR-Primer</one> sollten mindestens wie lange sein? Etwa <one>17 Nukleotide lang</one>.
+- When do we have to use <one>degenerate PCR primers</one>? When we <one>wish to target an unknown gene</one> (in <two>another organism</two>).
+- Allgemein: ein <one>Primer</one> für die PCR sollte am Ende was besitzen? Zwei bis drei <one>GC-Basenpaare</one>, zwecks höherer Stabilität.
+- The DamID method makes use of what kind of PCR? It makes use of a "methyl PCR".
+- Primer-Länge bei der PCR (von-bis)? 20bp-30bp, aber nicht kürzer, da diese Sequenzen ansonsten zu oft in Genen zu finden sind.
+- The TAQ polymerase has a terminal transfererase activity. In order to make use of it, we may require PCR fragments with an A-overhang or T-overhang. Name two ways how to prepare these. A: (1) Using restriction enzymes such as XcmI, which will cut at that. (2) Treating a blunt end vector with TAQ and dTTP
+- PCR requires primers. These primers must be complementary to ...? The PCR primers must be complementary to the 3' ends of each of the sense and anti-sense strand of the DNA target.

data/lib/studium/exam_topics/pentosephosphatweg

@@ -0,0 +1,61 @@
+# =========================================================================== #
+# === Der Pentosephosphatweg
+# =========================================================================== #
+
+- Nenne <one>ein Epimer</one> zu Ribulose-5-phosphat (letzteres ist Teil des Pentosephosphatweges). A: <one>Xylulose-5-phosphat</one>.
+- Was ist <one>das Startmolekül</one> im <two>oxidativen Pentosephosphatweg</two>? <one>Glucose-6-phosphat</one>. URL: https://de.wikipedia.org/wiki/Pentosephosphatweg#Oxidativer_Teil
+- Im <one>Pentosephosphatweg</one> kann Ribulose-5-Phosphat über die Pentose-5-phosphat-Epimerase in welches Substrat konvertiert werden? In <one>Xylulose-5-Phosphat</one>.
+- Die <one>Transketolase</one>, die im Pentosephosphatweg zum Einsatz kommt, <two>überträgt C2-Einheiten</two>. <three>Welches Coenzym verwendet dieses Enzym</three>? <one>Thiaminpyrophosphat</one>.
+- Im <one>Pentosephosphatweg</one> wird <two>NADPH erzeugt</two>, und zwar <three>zwischen welchen zwei Substraten</three>? (1) <one>Glucose-6-phosphat</one> (2) <one>Ribulose-5-phosphat</one>
+- <one>Warum</one> benötigt die Zelle den <two>Pentosephosphat-Zyklus</two>? Dieser Stoffwechselweg stellt <one>Pentosephosphate</one> (== Ribose-5-Phosphat) für die Synthese von Nukleotiden bereit. Zudem liefert er Redox-Äquivalente in Form von NADPH.
+- Der <one>Pentosephosphatweg</one> gewinnt aus dem Ausgangsstoff Glucose-6-phosphat welchen Zucker? Die <one>Pentose</one> <two>D-Ribose</two>.
+- Die <one>oxidative Phase des Pentosephosphatwegs</one> <two>beginnt mit ... </two>? Mit einer Wasserstoffabspaltung vom C1- des Glucose-6-phosphats.
+- <one>Welcher wichtiger Zucker</one> wird im Pentosephosphatweg synthetisiert? <one>D-Ribose</one>.
+- Wann verwendet die Zelle eher die nichtoxidative Phase des Pentosephosphatwegs? Wenn die Zelle wesentliche mehr NADPH als Ribose-5-phosphat benötigt.
+- Welche Zellen vor allem, in eukaryoten Organismen, benötigen den Pentosephosphatweg? Zellen die stark proliferieren.
+- Nenne ein Heptose-Produkt der <one>Transketolase</one>, das im Pentosephosphatweg synthetisiert wird. A: <one>Sedoheptulose-7-phosphat</one>.
+- <one>Warum</one> wird der <two>Pentosephosphatweg</two> auch <three>Pentosephosphat-Shunt</three> genannt? Da die <one>Zwischenprodukte</one> <two>Glycerinaldehyd-3-phosphat</two> sowie <two>Fructose-6-phosphat</two> einen Quereinstieg - aka <three>shunt</three> - die Glykolyse ermöglichen.
+- In der <one>nicht-oxidativen Phase des Pentosephosphatweg</one> werden welche <two>zwei (glykolytischen) Zwischenprodukte erzeugt</two>? (1) <one>Fructose-6-Phosphat</one> (2) <one>Glycerinaldehyd-3-Phosphat</one>
+- Was ist das <one>zentrale Inputmolekül</one> - also das Startmolekül - im <two>Pentosephosphat-Weg</two>? <one>Glucose-6-Phosphat</one>.
+- Kommt es im Zuge des Pentosephosphatweges zu einer <one>Decarboxylierung</one>? Ja - denn die <one>Glucose-6-phosphat</one> hat ein C-Atom mehr als <two>Ribulose-5-phosphat</two>.
+- Welche <one>Phasen</one> hat der <lightseagreen>Pentosephosphatweg</lightseagreen>? (1) <one>oxidative     Phase</one> (2) <one>nichtoxidative Phase</one>
+- Die <one>oxidative Phase</one> des <two>Pentosephosphatweges</two> ähnelt welch anderem Stoffwechselweg? Dem <one>Entner-Doudoroff-Weg</one>.
+- Beim <one>Pentosephosphatweg</one> wird im <two>oxidativen Weg</two> <three>welche Substanz gebildet</three>? <one>Ribulose-5-phosphat</one>. (Dabei wird auch NADPH gebildet.)
+- Im <one>Pentosephosphatweg</one> nimmt die <two>Pentose-5-phosphat-Epimerase</two> Ribulose-5-phosphat als Substrat und erzeugt ... ? <one>Xylulose-5-phosphat</one>.
+- Die erste Reaktion im Pentosephosphatweg wird durch welches Enzym katalysiert? Durch die <one>Glucose-6-phosphat-Dehydrogenase</one>.
+- <one>Vorläufer</one> von <two>Ribulose-5-Phosphat</two> im Pentosephosphatweg? <one>Gluconat-6-Phosphat</one>. URL: https://de.wikipedia.org/wiki/Glucose-6-phosphat
+- Im Pentosephosphatweg wird die Synthese einer <one>C4</one> und einer <one>C6-Einheit</one> <two>durch welches Enzym katalyisert</two>? <one>Transaldolase</one>.
+- Der <one>Pentosephosphatweg</one> <two>erzeugt generell welche zwei Substanzen</two>? (1) <one>NADPH</one> (2) <one>C₅-Kohlenhydrate</one>
+- Welche <one>zwei Enzyme</one> des <two>Pentosephosphatwegs</two> <three>erzeugen NADPH</three>? (1) <one>Glucose-6-phosphat Dehydrogenase</one> (2) <one>Gluconat-6-phosphat-Dehydrogenase</one>
+- Schlüsselenzym des <one>Pentosephosphatweges</one>? <one>Glucose-6-phosphat-Dehydrogenase</one>.
+- <one>Welcher C7-Körper</one> entsteht im Zuge des Pentosephosphatweges? <one>Sedoheptulose-7-phosphat</one>.
+- Warum der Name <one>Pentosephosphatweg</one>? Da das Hauptprodukt eine Pentose ist: <one>Ribulose-5-phosphat</one>.
+- Wieviel <one>NADPH</one> wird im Pentosephosphat-Weg erzeugt? <one>2</one>.
+- Zellulär betrachtet: <one>wo</one> findet der <two>Pentosephosphatweg</two> statt? Im <one>Cytosol</one>. URL: https://de.wikipedia.org/wiki/Pentosephosphatweg
+- <one>Welches Enzym</one> verknüpft den <two>Pentosephosphatweg</two> mit der <two>Glykolyse</two>? Die <one>Transketolase</one>. URL: https://de.wikipedia.org/wiki/Transketolase
+- Was ist das <one>Schlüsselenzym des Pentosephosphatweges</one>? Die <one>Glucose-6-Phosphat-Dehydrogenase</one>.
+- Ausgangsverbindung des <one>Pentosephosphatweges</one>? <one>Glucose-6-Phosphat</one>.
+- Im Zuge des <one>Pentosephosphatzyklus</one>, bei der Isomerisierung von <two>Ribulose-5-Phosphat</two> zu <two>Ribose-5-Phosphat</two>, entsteht welches Intermediat? Das <one>Endiol-Intermediat</one>.
+- Mit Hilfe des <one>Pentosephosphatweges</one> können Kohlenhydraten wie Glucose verwertet werden. <three>Welches Reduktionsmittel</three> wird dabei gebildet? <one>NADPH</one>. URL: https://de.wikipedia.org/wiki/Nicotinamidadenindinukleotidphosphat
+- Die <one>nichtoxidative Phase</one> <two>des Pentosephosphatwegs</two> ... Kohlenhydrate. A: <one>interkonvertiert Kohlenhydrate</one>. []
+- <one>In welcher Phase</one> erzeugt der <two>Pentosephosphatweg</two> <three>NADPH</three>? In der <one>oxidativen Phase</one>. URL: https://de.wikipedia.org/wiki/Pentosephosphatweg []
+- Das <one>erste Enzym im Pentosephosphatweg</one> <two>ist ... </two>? die <one>Glucose-6-phosphat-Dehydrogenase</one>. URL: https://de.wikipedia.org/wiki/Glucose-6-phosphat-Dehydrogenase []
+- In der <one>oxidativen Phase des Pentosephosphatwegs</one> wird <two>... erzeugt</two>. A: <one>NADPH</one>. []
+- Der <one>Pentosephosphatweg</one> <two>besteht aus wievielen Phasen</two>? Aus <one>zwei</one>. []
+- <one>Pro Durchlauf</one> erzeugt der <two>Pentosephosphatweg</two> <three>wieviele NADPH</three>? <one>2</one>. []
+- Allgemein, im <one>Pentosephosphatweg</one> wird <two>welches Reduktionsmittel gebildet</two>? <one>NADPH</one>. []
+- Im <one>Pentosephosphatweg</one>, <two>in der nichtoxidativen Phase</two>: ist die Isomerisierung von Ribulose-5-phosphat in Ribose-5-phosphat reversibel? <one>Ja</one>, wie auch alle anderen Reaktionen der nichtoxidativen Phase des Pentosephosphatwegs. []
+- Wird <one>Ribose-5-phosphat</one> im <two>Pentosephosphatweg</two> synthetisiert? <one>Ja</one>. []
+- Was geht in der <one>oxidativen Phase</one> des Pentosephosphatweges verloren? <one>CO₂</one>. []
+- Sind die Teilreaktionen im zweiten Abschnitt des Pentosephosphat-Zyklus, also im <one>nicht oxidativen Teil</one>, <two>reversibel</two>? <one>Ja</one>. []
+- Ein einzelnes <one>Glucose-6-phosphat Molekül</one> <two>kann über den Pentosephosphatweg</two> <three>wieviel Moleküle NADPH liefern</three>? <one>Zwölf</one> (<two>12</two>). []
+- Ist der <one>Pentosephosphatweg</one> <two>wichtig für die Gluconeogenese</two>? <one>Ja</one> - die Endprodukte Glycerinaldehyd-3-phosphat und Fructose-6-phosphat können für die Gluconeogenese herangezogen werden. []
+- Entlässt der Pentosephosphatweg CO₂? <one>Ja</one>. []
+- Im <one>oxidativen Teil des Pentosephosphatwegs</one> <two>entstehen wieviele NADPH Moleküle pro Durchlauf</two>? <one>Zwei</one>. []
+- Der <one>Pentosephosphatweg</one> <two>ist mit welchem anderen metabolischen Zyklus am stärksten assoziiert</two>? Mit der <one>Glykolyse</one>. []
+- Im <one>Pentosephosphatweg</one> werden <two>in der nichtoxidativen Phase</two> Kohlenhydrate mit wievielen Kohlenstoffatomen synthetisiert? (1) <one>C3</one> (2) <one>C4</one> (3) <one>C5</one> (4) <one>C6</one> (5) <one>C7</one> []
+- Startmolekül des <one>Pentosephosphatweges</one>? <one>Glucose-6-Phosphat</one>. URL: https://de.wikipedia.org/wiki/Pentosephosphatweg#Oxidativer_Teil []
+- Das Enzym <one>Glucose-6-phosphat-Dehydrogenase</one>, <two>zentral für den Pentosephosphatweg</two>, kann auf welchem Chromosom beim Menschen gefunden werden? Auf dem <one>X-Chromosom</one>. []
+- Der <one>Pentosephosphatweg</one> <two>ist eng mit welchem anderen Stoffwechselweg verknüpft</two>? Mit der <one>Glykolyse</one>. []
+- Der Begriff <one>Pentosephosphat-Shunt</one> bezieht sich auf welchen weiteren Stoffwechselweg? Auf die <one>Glykolyse</one>; Zwischenprodukte des Pentosephosphatwegs können für die Glykolyse herangezogen werden. []
+- Im <one>Pentosephosphatweg</one> erfolgt die Synthese welcher 3er <three>Pentosephosphate</three>? (1) <one>Ribulose-5-Phosphat</one> (2) <one>Ribose-5-Phosphat</one> (3) <one>Xylulose-5-Phosphat</one> (Mnemonic: Ribose, Ribulose, Xylulose + 5-Phosphat)

data/lib/studium/exam_topics/peroxisomes_glycosomes_and_lysosomes

@@ -0,0 +1,66 @@
+# =========================================================================== #
+# === Peroxisomes
+#
+# This should possibly be extended towards microbodies in general - but
+# since I needed this for an exam, I started with peroxisomes
+# specifically.
+# =========================================================================== #
+
+- How does the cell determine that some proteins have to be imported into the peroxisome? By making use of the peroxisomal targeting signal (PTS). This can be at the C-terminus or at the N-Terminus.
+- The <one>Zellweger phenotype</one> is due to a defect in peroxisomes. A mouse model is useful to study this disease. The PEX13 gene is one good candidate. How was the mouse genome modified to allow researchers to study this gene? A loxP-modified PEX13 gene was used via a conditional Cre recombinase-mediated inactivation of the Pex13 gene.
+- In humans: mutations in which gene, encoding a peroxisomal membrane protein necessary for peroxisomal protein import, can lead to the Zellweger phenotype? Mutations in the <one>PEX13 gene</one>.
+- Are <one>glyoxysomes</one> are specialized peroxisomes? Yes.
+- Was ist eine Lipidperoxidation? Eine Lipidperoxidation bezeichnet die oxidative Degradation von Lipiden. 
+- Name a major function of the peroxisome. A: The <one>breakdown of very long chain fatty acids</one> through <two>beta oxidation</two>.
+- If a cell has a plentiful supply of glucose, what could be assumed about the peroxisomes in such a cell? Only a few and small peroxisomes will be present - at the least this is the case in yeast.
+- <one>Peroxisomes</one> have how many biomembrane layers? Only one - thus they contain a <one>single biomembrane</one>.
+- When <one>plants</one> lack peroxisomes, what may be the consequence? They may no longer be able to produce the phytohormone <one>auxin</one>.
+- Are peroxisomes important for viruses? Yes, for some. For example, the <one>tTomato bushy stunt virus</one> will be unable to reverse transcribe its genome without peroxisomes.
+- Say that someone claims that peroxisomes are important for intelligence. Can we give an example to verify this claim? Yes - without peroxisomes we may see an <one>abnormal brain development</one>.
+- <one>Peroxisomes</one> were first described by Rhodin in which year? <one>1954</one>.
+- Novel Peroxisomal Proteins can be identified via PCP, which stands short for ... ? <one>Protein Correlation Profiling</one>.
+- Novel Peroxisomal Proteins can be identified via ... ? <one>2D-PAGE</one>.
+- <one>Peroxisomes</one> can be purified via ... ? <one>density gradient centrifugation</one>.
+- <one>Peroxisomes</one>  were first identified by de Duve in ... ? <one>1965</one>.
+- Peroxisomes have how many membranes? One.
+- Is the <one>PEX19-receptor</one> soluble? Yes.
+- Do peroxisomes have an <one>endosymbiotic origin</one>? No.
+- Are <one>peroxisomes</one> an organell? Yes. They are also known as <one>a microbody</one>.
+- The three aminoacids of the <one>PTS</one> are typically ... ? <one>SKL</one>.
+- Do <one>peroxisomes</one> contain DNA? No.
+- Can we find <one>amino acid catabolism in peroxisomes</one>? Yes.
+- <one>Peroxins</one> are genes encoding proteins involved in the biogenesis of peroxisomes. They are abbreviated how? Via <one>PEX</one>.
+- Peroxisomes contain <one>enzymes</one> for the degradation of ... ? <one>H2O2</one>.
+- We can typically <one>stain peroxisomes</one> via ... ? DAB (diamino-benzidine).
+- <one>PEX3</one>, an integral membrane protein, binds to ... ? <one>PEX19</one>.
+- Where in a cell will <one>peroxisomal proteins</one> be synthesized? In the <one>cytoplasm</one>; they must then be directed into the peroxisome, via the <royalblue>PTS</royalblue> (peroxisomal targeting signal).
+- What <one>gradient</one> can be found in a peroxisome? A <one>pH gradient</one> across the membrane.
+- Who creates the <one>peroxisomes</one>? The <one>endoplasmic reticulum</one> (ER).
+- The PEX19-receptor, important for peroxisomes, has a terminal -CAAX group. What is this used for? As signal for <one>farnesylation</one>.
+- Does the PEX19-receptor bind all peroxisomal membrane proteins? Yes.
+- Peroxisomal targeting signal requires a mPTS (membrane Proteins), but also a ... TMD. What does this abbreviation stand for? <one>Transmembrane domain</one> (TMD).
+- Does <one>receptor recycling</one> occur during transport of proteins into the peroxisome? Yes.
+- We have the peroxisomal targeting signals PTS1 and PTS2. Which one is on the N-Terminus? <one>PTS2</one>.
+- Does the <one>Mito-Signal</one> dominate over the <one>PTS1 Signal</one>, if it is in the same protein? Yes.
+- Can the peroxiomes import oligomerized proteins? Yes.
+- Which PTS contains a nonapeptide near its N-terminus? PTS2.
+- Name the receptors for <one>PTS1</one> and <one>PTS2</one>. A: (1) PTS1: <one>PEX5</one> (2) PTS2: <one>PEX7</one>
+- How many peroxisomal targeting signals are known? About three: PTS1, PTS2 and PTS3 - although there is insufficient data to ascertain that a PTS3 signal exists.
+- Name one big peculiarity of the peroxisomal matrix protein import. A: <one>Folded proteins</one> will be imported.
+- Name three general metabolic pathways that can take place in peroxisomes, or where peroxisomes may be very important. A: (1) <one>fatty acid oxidation</one> (2) <one>H2O2 metabolism</one> (3) <one>lipid biosynthesis</one>
+- Are <one>Microbodies</one> like <one>Microsomes</one>? No.
+- <one>Peroxisomes</one> may also contain RNS, which stands for ... ? <one>Reactive Nitrogen Species</one>.
+- Most peroxisomal matrix proteins contain a short sequence, usually three amino acids, which part: <one>amino tail</one> or <one>carboxy tail</one>? At the carboxy tail of the protein.
+- Name a very important role that the peroxisomes fulfill. A: Peroxisomes are involved in the catabolism of very long chain fatty acids.
+- In <one>peroxisomes</one>: what is PTS? This is a peroxisomal targeting signal.
+- The PTS of proteins that are to be relocated into the peroxisome typically contain how many aminoacids? 3.
+- Name a disease where we can find no functional peroxisomes. A: The <one>Zellweger syndrom</one>.
+- In regards to peroxisomes: what does the abbreviation PBD stand for? <one>Peroxisome biogenesis disorders</one>.
+- What is Acatalasemia? This is a condition characterized by very low levels of the enzyme <one>catalase</one>.
+- The <one>ghost peroxisomal phenotype</one> can be seen upon which defect? When there is no (proper) protein import.
+- What are <one>peroxins</one>? This refers to <one>genes encoding a protein that is involved in the biogenesis of peroxisomes</one>.
+- Name the three P-Peroxins. A: <one>Pas, Per, Pim</one>.
+- Like many other organelles, peroxisomes communicate through ... ? <one>membrane contact sites</one>.
+- Peroxisomal growth, positioning, and lipid metabolism involves contacts with ... ? <one>the endoplasmic reticulum</one>.
+- When pathogenic plant fungi have no peroxisomes, what may be the consequence of this? There may be no infection without peroxisomes.
+- Glycosomes can typically be found in ... ? <one>Protozoa</one>.