studium 0.18.7

data/lib/studium/exam_topics/stickstofffixierung

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+# =========================================================================== #
+# === Stickstofffixierung
+#
+# This is also known as "nitrogen-fixation".
+# =========================================================================== #
+
+- Most nitrogenases containing molybdenum are <one>sensitive to O₂</one>, but there are examples of nitrogenases containing molybdenum that are <two>insensitive to O₂</two>. <three>Give one such example for an organism containing such a nitrogenase</three>. A: <one>Streptomyces thermoautotrophicus</one>.
+- Was enthält die <one>alternative Nitrogenase</one> anstatt <two>Molybdän</two>? <one>Vanadium</one> - oder <one>Eisen</one>.
+- Name <one>two different clusters</one> that can be found in the <two>nitrogenase</two>. A: (1) The <one>[4Fe-4S] cluster</one> (2) The <one>FeMo-co cluster</one>
+- <one>Industrial nitrogen</one> <two>fixation</two> uses ... ? The <one>Haber process</one>, also called <one>Haber-Bosch process</one>. URL: https://en.wikipedia.org/wiki/Haber_process
+- Do <one>nitrogenases</one> exist that <two>do not use molybdene</two> as cofactor? <one>Yes</one> these are called <two>alternative nitrogenases</two>.
+- <one>Stickstofffixierung</one> wurde beobachtet in einer <two>pH-Spanne</two> von ... bis ... ? Von <one>pH 2 bis pH 10</one>.
+- The <one>heterocysts</one> used by some <two>cyanobacteria</two> <three>lose what upon becoming heterocysts</three>? Their <one>ability for photosynthetic capacity</one>.
+- Does the <one>heterocyst</one> <two>produce O₂</two>? <one>No</one> it does not.
+- Sind die <one>Bacteroide</one> <two>in den Leguminosen</two> vollständig in ihrer Energieversorgung durch die Pflanze abhängig? <one>Ja</one>.
+- Besitzt der <one>Nitrogenase-Komplex</one> <two>mehrere Redoxzentren</two>? <one>Ja</one>.
+- Wieso kann die <one>Nitrogenase</one>, auf die die Leguminosen indirekt einwirken, Stickstoff fixieren, trotz Sauerstoffempfindlichkeit der Nitrogenase? In den <one>Wurzelknöllchen</one> <two>schützt Leghämoglobin die Nitrogenase</two>, durch O2-Bindung.
+- <one>Which part of the nitrogenase</one> actually <two>fixes nitrogen</two>? The <one>FeMo-co cofactor</one>.
+- Alle <one>Nitrogen-fixierenden Organismen</one> <two>müssen einen Mechanismus besitzen um die Konzentration an Sauerstoff niedrig zu halten</two>. Warum? A: Weil das Enzym <one>Nitrogenase</one> <two>sehr sensitiv gegenüber Sauerstoff ist</two>.
+- Entsteht bei der Stickstofffixierung <one>Hydrazin</one>? <one>Ja</one>, und zwar <two>genau bevor Ammoniak produziert wird</two>.
+- Why is the <one>nitrogenase</one> <two>extremely sensitive towards oxygen</two>? Because of the large reducing power needed to make NH4⁺. Thus, cells can fix nitrogen only in an anaerobic environment.
+- Is <one>the inside of a heterocyst</one> <two>anoxic</two>? <one>Yes</one>.
+- <one>How</one> is the state within a plant cell called caused by Rhizobia infiltrating the plant cell? <one>Bacteroid state</one>.
+- Nenne <one>zwei mögliche Donoren für Elektronen</one> die von der Dinitrogenase-Reduktase verwendet werden können. A: (1) <one>Ferredoxin</one> (2) Flavodoxin
+- <one>Which part</one> of the nitrogenase binds ATP? The <one>dinitrogenase reductase</one>.
+- <one>Leghämoglobin</one> ist welch anderem Protein ähnlich? <one>Myoglobin</one>.
+- Are there <i>Archaea</i> that <two>can fix nitrogen</two>? <one>Yes</one> - for instance in <two>Methanococcus</two>.
+- Gibt es für die Leguminosen einen konkreten Vorteil durch ihre Symbiose mit Knöllchenbakterien? Ja - Leguminosen können dadurch auch in unfruchtbaren Böden gedeihen. Dies stellt somit einen <one>Selektionsvorteil</one> dar.
+- Enthält <one>Leghämoglobin</one> Eisen? Ja.
+- Der Fe₄-S₄-Cluster der Nitrogenase findet sich in welcher Untereinheit? In der <one>Dinitrogenase-Reduktase</one>.
+- Can <one>eukaryotes</one> <two>fix nitrogen</two>? <one>No</one>.
+- <one>Welche Person</one> <two>entdeckte die ersten stickstofffixierenden Bakterien</two>? <one>Martinus Beijerinck</one>. URL: https://de.wikipedia.org/wiki/Martinus_Willem_Beijerinck
+- Die <three>Nitrogenase</three> besteht aus <one>n Komponenten</one>? <one>Zwei</one>.
+- <one>Nitrogen fixation</one> <two>requires how reduction cycles through nitrogenase</two>? <one>Four</one>.
+- <one>Which assay</one> <two>can be used to detect nitrogen fixation</two>? The <one>acetylene reduction assay</one>.
+- The <one>nitrogenase</one> <two>is protected via ... </two>? Name three different strategies employed here. A: <one>Slime formation around the cell</one>. (2) Respiration. (3) Specialized cells (<one>heterocysts</one>) with thick cell walls in some cyanobacteria.
+- <one>N₂ fixation</one> requires the enzyme ... ? <one>Nitrogenase</one>. URL: https://de.wikipedia.org/wiki/Nitrogenase
+- <one>Warum</one> ist die <two>ATP-Hydrolyse</two> <three>wichtig für die Nitrogenase</three>? Die <one>ATP-Hydrolyse</one> <two>zwingt die Nitrogenase in eine energireiche Konformation</two>, in der das Redoxpotenzial der elektronenübertragenden FeS-Zentren extrem negativ wird.
+- <one>Welches Enzym</one> ist für die <two>Stickstofffixierung</two> am wichtigsten? Die <one>Nitrogenase</one>. URL: https://de.wikipedia.org/wiki/Nitrogenase
+- The most important enzyme for <one>N₂ fixation</one> is ... ? The <one>nitrogenase</one>. URL: https://en.wikipedia.org/wiki/Nitrogenase
+- Die <one>Rhizobien</one> (also die 'Knöllchenbakterien'), die atmosphärischen Stickstoff fixieren können, <two>gehören zu welcher phylogenetischen Bakteriengruppe</two>? <one>Rhizobien</one> gehören zu den <two>Alphaproteobacteria</two>. URL: https://en.wikipedia.org/wiki/Alphaproteobacteria
+- Die meisten <one>Nitrogenasen</one> können welche Substanz reduzieren? <one>Acetylene</one>.
+- The <one>FeMo protein</one> <two>binds 2 H⁺ and emits ... </two>? <one>H₂</one>.
+- Was wird bei der <one>Stickstofffixierung</one> pro fixiertem <three>N₂</three> freigesetzt? <one>H₂</one>.
+- Is <one>ATP</one> <two>required for nitrogen fixation</two>? <one>Yes it is</one>. The <two>dinitrogenase reductase</two> <three>requires two ATP per cycle of electron transfer</three>.
+- Bei der Stickstoffixierung: <one>welche Aufgabe hat Komponente II der Nitrogenase</one>? Die <one>Komponente II</one> liefert die Elektronen.
+- The <one>first nitrogenase complex isolated</one> came from <i>Clostridium pasteruianum</i>, from the DuPont Laboratory, <two>in which year</two>? In <one>1960</one>.
+- <one>Stickstofffixierende Bakterien</one> gehen eine Symbiose mit <two>Leguminosen</two> ein. <three>Nenne ein Beispiel als pflanzlichen Vertreter hierzu</three>. A: Die <one>Sojabohne</one>. URL: https://de.wikipedia.org/wiki/Sojabohne
+- <one>Nitrogen fixation by bacteria</one> typically creates which compound, as the <two>final product</two>? <one>NH₃</one>.
+- Die <one>Nitrogenase</one> besitzt den sogenannten <two>P cluster</two>, der eine wichtige Aufgabe in Bezug auf den FeMo cluster hat. Welche ist dies? Elektronen werden durch den P cluster an den FeMo cluster geliefert.
+- <one>In which bacteria</one> is the <two>nitrogenase</two>, during nitrogen fixation, <three>compartmentalized</three>? In <one>cyanobacteria</one>, such as <i>Anabaena spiroides</i>. The nitrogenase can be found in the heterocyst.
+- <one>Heterocyst development</one> is directed by a complex genetic program induced by ... ? <one>Nitrogen starvation</one>.
+- Why is photosynthesis turned off in heterocysts? Because these microorganisms wish to maintain anaerobic conditions in these heterocysts.
+- Does the <one>dinitrogenase</one> in the nitrogenase have free intermediates during its reaction? No.
+- Quelle der Reduktionskraft bei der <one>Stickstoffixierung</one>? <one>Reduziertes Ferredoxin</one>.
+- <one>Ferredoxin</one> (ein FeS-Protein) ist für die Stickstoffixierung wichtig; <two>bei Eisenmangel</two> kann es jedoch durch ... ersetzt werden. A: <one>Flavodoxin</one>.
+- <one>Nitrogenase</one> typically contains <two>the FeMo cluster</two>. This cluster requires electrons delivered from another cluster, though. <three>Which cluster is that</three>? The <one>P cluster</one> (a Fe2S cluster) provides electrons to the FeMo cluster.
+- The enzyme <one>nitrogenase</one> contains the <two>FeMo-co cofactor</two>. <three>Where can the Molybdene be found within that enzyme</three>? It is <one>just about central</one> in that cofactor - at the least towards one of its end.
+- The <one>metal cluster</one>, that is Fe₇S₉Mo (FeMo-co cluster), is held in place not only by two aminoacids of the nitrogenase, but also by coordination with a molecule of ... ? <one>Homocitrate</one>.
+- <one>Alternative nitrogenases</one> are similar to the regular nitrogenases, except for another metal in place of molybdenum (in FeMo-co). <two>Which one may be the other metal used here</two>? <one>Fe</one> (aka iron).
+- The <one>FeMo-co cluster</one> not only <two>binds homocitrate</two>, but two amino acid residues of the nitrogenase, which are ... which two aminoacids? (1) <one>Cysteine</one>  (at <two>position 275</two>) (2) <one>Histidine</one> (at <two>position 442</two>)
+- For <one>nitrogen fixation found in land plants</one>: <two>name a bacterium that begins with the letter B and grows in nodules on these plants</two>. A: <one>Bradyrhizobium japonicum</one>. URL: https://en.wikipedia.org/wiki/Bradyrhizobium_japonicum
+- Why is the enzyme <one>nitrogenase</one> so sensitive towards oxygen? Because of the large reducing power needed to make NH4⁺.
+- One consequence of <one>nitrogenase structure</one> of nitrogen-fixing organisms is ... ? The nitrogenase <one>requires molybden</one> - <two>and so do the organisms that do fix nitrogen</two>. Some alternative nitrogenases require vanadium instead of molybdenum, though, thus bypassing a need for molybdenum.
+- <one>Nitrogenase</one> wurde im Jahre 1960 aus dem Bakterium ... isoliert. A: <one>Clostridium pasteruianum</one>.
+- Do <one>trees</one> <two>make use of nitrogen fixation</two> via symbiosis? <one>Yes</one>, such as can seen in <two>alder trees</two>.
+- <one>Nitrogenase</one> <two>is sensitive to ... </two>? <one>O₂</one>.
+- Nenne <one>Input</one> und <one>Output</one> der <two>Nitrogenase</two>. A: (1) <one>Input</one>: <two>N₂</two>. (2) <one>Output</one>: <two>NH₄</two>.
+- The <one>NodD factor</one> for Legume-root symbiosis is induced by ...? <one>Flavonoids</one> <two>excreted by plants</two>.
+- <one>Nach welchem Wirkprinzip</one> kann man die Nitrogenase-Aktivität messen? Die Nitrogenase konvertiert <one>Ethin</one> in <one>Ethen</one>. Die Menge an produziertem Ethen kann gemessen werden.
+- <one>Where</one> in particular could free-living nitrogen-fixing bacteria be found? In the <one>rhizosphere</one>, a region roughly 2 millimeters from the plant root.
+- The <one>nitrogen starvation sigma factor</one> is ... ? <one>sigma-54</one>. URL: https://www.nature.com/articles/nrmicro2058
+- Nenne den genauen (stöchiometrisch korrekten) <one>Input</one> und <one>Output</one> der <two>Nitrogenase</two>. A: (1) N₂ ist Input (2) 2x NH₃ (Ammoniak) ist Output
+- In regards to <one>alternative nitrogenases</one>: <two>what suppresses their synthesis</two>? The presence of <one>molybdenum</one>.
+- <one>Welches Gerät</one> braucht man um die Nitrogenaseaktivität von Pflanzen zu messen? Mit Hilfe eines <one>Gaschromatographen</one>.
+- <one>Which compounds</one> can <two>Nitrogenase</two> reduce? (1) <one>N₂</one> (2) <one>acetylene</one>
+- Die <one>Nitrogenase</one> kann auch durch eine <two>Schleimschicht</two> vor O₂ geschützt werden. <three>Nenne ein Bakterium das diese Strategie verwendet</three>. A: <one>Azotobacter vinelandii</one>.
+- Die <one>Nitrogenase</one> braucht welchen Kofaktor? <one>Molybdän</one>.
+- <one>Which gene product</one> is the <two>regulator of nodulation</two>? <one>nodD</one>.
+- <one>Nitrogen fixation</one> works up towards a temperature of at the least ... n °C? <one>92°C</one>.
+- <one>Which regulon</one> is important in <two>nitrogen fixation</two>? The <one>nif regulon</one>. URL: https://en.wikipedia.org/wiki/Nif_regulon
+- <one>Who</one> are <two>the best-known nitrogen-fixing bacteria</two>? The <one>Rhizobia</one>. URL: https://en.wikipedia.org/wiki/Rhizobia
+- <one>Nitrogenase</one> can be shut down not only by O₂, but also by which other molecule? <one>NH₃</one>.
+- What may <one>inhibit nitrogen fixation</one>? <one>Oxygen</one>.
+- Pro <one>N₂-Molekül</one> das fixiert wird benötigen Bakterien <three>n ATP Moleküle</three>? <one>16 ATP</one>. URL: https://de.wikipedia.org/wiki/Nitrogenase#Katalysierte_Reaktion
+- Die <one>Nitrogenase</one> (a nanomachine) verwendet was für einen Cofaktor? <one>Iron-Molybdenum</one> im Verhältnis 7:1, verbunden mit Schwefel-Atomen.
+- Why do some <one>nitrogen-fixing bacteria</one> <two>make use of alternative nitrogenases</two>? These <one>alternative nitrogenases</one> often <two>function as a backup system</two>, <three>to support nitrogen fixation when molybdenum is unavailable in their habitat</three>.
+- Wird im Zuge der Stickstofffixierung <one>Hydrazin</one> gebildet? Ja. URL: https://de.wikipedia.org/wiki/Hydrazin
+- <one>Welches Enzym</one> ist für <two>stickstoffoxidierende Mikroorganismen</two> extrem wichtig? Die <one>Nitrogenase</one>. URL: https://de.wikipedia.org/wiki/Nitrogenase
+- Definiere den Begriff <one>Stickstofffixierung</one>. A: Verwendung von <one>N₂</one> als <two>biosynthetischer Stickstoffquelle</two>.
+- <one>Which bacterium</one> <two>can fix N₂ at full O₂ tension</two>? <one>Frankia cells</one>. They do this by localizing the nitrogenase in terminal swellings on the cells, in vesicles. These vesicles have thick cell walls, which help protect against O₂.

data/lib/studium/exam_topics/structural_bioinformatics

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+# =========================================================================== #
+# === Structural Bioinformatics tag
+#
+# Everything about structural bioinformatics.
+#
+# Also Gene Ontology and Structural Bioinformatics. 
+# =========================================================================== #
+
+- When we make use of "homology-based annotation transfer", what should we keep in mind? It <one>may produce wrong results</one>.
+- What means <one>Shapely</one> in <two>Rasmol</two>? That <one>each aminoacid gets its own colour</one>.
+- The <one>PDB database</one> has approximately how many unique protein structures? More than <one>3000</one>.
+- Name the <one>three categories of GO</one> (<two>Gene Ontology</two>). A: (1) "Molecular Function" (2) <one>Biological Process</one> (3) "Cellular Component" URL: https://en.wikipedia.org/wiki/Gene_ontology
+- Fitness landscape is a 2D-diagram. It has two axes, which are ... ? (1) fitness (2) sequence space
+- Does the genetic algorithm eliminate the worst candidates (lowest fitness)? Yes.
+- Why is the Monte Carlo algorithm used in sequence prediction? Because we can reach better local minima in sequence space.
+- In PyMOL, when we see <one>by ss</one>, what is meant here? This means <one>"by secondary structure"</one>, e. g. the use case of colourizing "alpha-helices" and "beta-sheets".
+- Give an example for a software program that can be used in order to create Ramachandran plots. A: DeepView from ExPASy. URL: https://spdbv.vital-it.ch/
+- Structural genomics starts with ... ? A DNA sequence - thus, we have to obtain the genomic DNA sequence first.
+- <one>FunFams</one> stands short for ... ? Functional families. URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531114/
+- How could we identify relationships of homology between different proteins? Via <one>BLAST search</one>.
+- Give a reason why <one>algorithms</one> are harder to implement in structural bioinformatics than in regular DNA/RNA bioinformatics. A: Unlike sequences such as DNA polymers, structural data is not linear and therefore is not easily amenable to algorithms based on strings.
+- The main repository of protein structures is ... ? PDB: The <one>Protein Data Bank</one>.
+- What are <one>lipocalins</one>? A diverse family of <violet>ligand binding proteins</violet>.
+- What do we mean with an <one>energy landscape</one>? This refers to the conformation that are possible for a given protein.
+- One of the most important stages in the <violet>drug discovery process</violet> is the ability <one>to identify</one> ... on proteins? "ligand-binding sites".
+- The <one>PDB website</one> provides a number of services for structure submission and data searching and retrieval. How is its "web interface" called? "Structure Explorer".
+- Die <one>BRENDA Datenbank</one> umfasst wieviele <one>Enzyme</one>? Zumindest "6500".
+- The "Protein Data Bank" has <one>how many</one> protein structures archived, in about 2014? More than "30.000".
+- PyMOL has a sequence called <one>ASHLC</one>. What do these letters stand for? (1) Actions (2) Show (3) Hide (4) Label (5) Color
+- <one>Walter Gilbert</one> said something interesting about bioinformatics once. What was it? "Use computational tools - or become obsolete."
+- In general, in a program such as <one>PyMOL</one>, what do we mean with a "ribbon"? This is a connection between adjacent C-alpha atoms.
+- From the point of view of <one>structural bioinformatics</one>, which two aminoacids are very important? (1) "glycine" (2) "proline"
+- What is the main goal of "strutural genomics"? Structural Genomics attempts <one>to predict the 3D structure of all proteins</one> encoded in a given genome.
+- Name a <one>database</one> that describes all known "protein domain structures". A: "CATH". URL: http://www.cathdb.info/
+- Bioinformatic tools can be based on which <one>two aspects</one>? (1) sequence-based (2) structure-based
+- <one>Structural genomics</one> attempts to solve the structure of at least one representative protein for each ... ? For "each existing structural fold".
+- Identification of binding sites in proteins is very important for the "drug discovery process". We can then "identify ligand-binding sites on proteins". This is especially important for <one>new drugs</one>, and new potential ligands, where we do not yet have any prior knowledge. Name three different general ways, from the point of view of structural bioinformatis. A: (1) "HIPPO" (2) "SURFNET" (3) "SIRFNET"
+- <one>PyMOL</one> has the "chainbow" colour scheme. If we see a dark-blue segment, what do we know? That this is the "N-terminus" (Aminoterminus).
+- Why may <one>structural bioinformatics</one> be important in the future? Because it is important to "discover new druggable proteins".
+- What is meant with the term "sequence motif recognition"? Certain residues code for a specific function, e. g. the <one>KDEL retention signal</one>. Examples are KDEL, HDEL and so forth.
+- The data format in <one>PDB</one> is very peculiar. Why may that be so? Partially because <violet>it is quite old</violet>, created in the early 1970s; but also because it was initially designed to be compatible with "FORTRAN programs".
+- How to view only one chain in "Rasmol"? Via "restrict 1-1000A".
+- The dihedral (torsional) angle is an angle between ... ? "two planes".
+- Can two identical polypeptide segments have a completely different three-dimensional structure? Yes.
+- Are "sequence-based tools" better than "structure-based tools", as far as bioinformatics is concerned? No - structure-based tools are better.
+- The PDB format has some limitations. Two alternative formats are mmCIF and MMDB. What do these abbreviations stand for? (1) "mmCIF": macromolecular crystallographic information file (2) "MMDB":  molecular modeling database file
+- What is meant with the term "protein space"? This means "all possible proteins".
+- Why are "inaccurate annotations in the database" a problem? Because this may "result from inaccurate predictions".
+- Why may "sequence motif recognition" produce wrong results? Because it is, in general, the "three-dimensional arrangement of the residues" that confer activity to a certain polypeptide moiety.
+- Name a "database for enzymes". A: "BRENDA", founded in the year "1987". URL: https://en.wikipedia.org/wiki/BRENDA#History
+- What may the "presence of a structural motif" indicate? The presence of a "common structural motif" may indicate "the presence of a certain binding site", related to the protein function.
+- We may wish to determine the function of new proteins through "structural bioinformatics". Name a big driver for this. A: Pharmacy, via "druggability" of targets.
+- Why do we use the "B-factor" in structural bioinformatic? We can determine the flexibility of each atom that way.
+- Name three different bioinformatics approaches to "predict protein function". A: (1) "Homology based methods" (2) "de-novo prediction of functional features" (3) "automated gene ontology (GO) prediction"