studium 0.13.1

data/lib/studium/exam_topics/stemcells

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+# =========================================================================== #
+# === STEMCELLS                                           (stem tag, stemtag)
+#
+# Alles über Stammzellen.
+#
+# Stem cells tag.
+# =========================================================================== #
+
+- Yamanaka won the Nobel Prize in Physiology or Medicine in which yearh? In <one>2012</one>.
+- How many transcription factors are necessary to transform human skin cells into cells that act like embryonic stem cells? <one>Four</one> (<two>4</two>) only.
+- Besitzen <one>humane, induzierte, pluripotente Stammzellen</one> ein <two>vollständiges Entiwcklungspotenzial</two>? Ja.
+- <one>Shinya Yamanaka</one> verwendete welche virale Gruppe um induzierte, pluripotente Stammzellen zu gewinnen? <one>Lentiviren</one> - es wurden daher <two>lentivirale Expressionsvektoren</two> verwendet.
+- <one>Shinya Yamanaka</one>'s Gruppe konnte im Jahre <two>2006</two> <three>welche somatischen Zellen</three> in pluripotente Stammzellen umprogrammieren? <one>Fibroblasten</one>.
+- Gibt es <one>humane, immortale embryonale Stammzellen</one>? Ja. 
+- Bei Stammzellen: was ist mit dem Begriff <one>immortal</one> gemeint? Das <one>diese Stammzellen prinzipiell unendlich vermehrbar sind</one>.
+- Sind <one>humane, pluripotente Stammzellen</one> <two>immortal</two>? Prinzipiell ja - <one>sie sind unendlich vermehrbar</one>.
+- Can we turn <one>ES Cells</one> into <two>Insulin Producing Cells</two>? Yes. []
+- In stem cell science: what is meant with the abbreviation <one>EG cells</one>? This refers to <one>Embryonic germ cells</one>. []
+- For <one>informed consent</one> in stem cell research, what testing to be done on the donors is especially important? <one>Histocompatibility testing</one>.
+- Name a role that <one>astrocytes</one> have. A: Astrocytes <one>produce substances that are tropic to neurons</one>.
+- Name <one>two features</one> that stem cells must have. A: (1) <one>self-renewal capacity</one> (2) <one>potency</one>
+- How do <one>cardiomyocytes</one> communicate with one another? Via <one>gap junctions</one>. []
+- Why are <one>induced stem cells</one> considered so useful? Because they may find use in regenerative medicine.
+- In stem cells: what is meant with the expression <one>the degree of plasticity</one>? This means whether a differentiated cell can change into another cell type. This is possible in an adult human, but is a rare event.
+- <one>Mesenchymal stem cells</one> (MSC) were first discovered where? In <one>bone marrow</one>.
+- Do <one>teratocarcinomas</one> contain tissues from <two>all three germ layers</two>? Yes. []
+- Between a <one>stem cell</one> and a <two>mature effector cell</two> we can find ... ? The <one>transient amplifying cells</one>.
+- For stem cell research: why may it be useful to consider learning more about the vascular system? Because <one>larger tissue engineered constructs need oxygen, nutrients, and thus, ultimately, also a</one> <two>vascular system</two>.
+- Give an example for a specific event that may <one>induce cell proliferation</one> followed by differentiation. A: <one>Trauma</one>.
+- For <one>angiogenesis</one>: the first growth factor to be produced is ... ? <one>bFGF - basic Fibroblast Growth Factor</one>.
+- <one>HPCs</one> are ... ? <one>Hematopoietic progenitor cells</one>. 
+- <one>Induced pluripotent stem cells (iPSCs)</one> were discovered by Takahashi and Yamanaka in what year? <one>2006</one>.
+- How many <one>cancer stem cells</one> arise? Through <one>mutational transformation of normal stem cells</one>:
+- <one>Tumor stem cells</one> may show that there is a correlation between ... ? Sem cells and tumorigenesis.
+- The <one>neoplastic proliferation of cancer stem cells</one> is likely to be driven by ... ? By <one>mutations that inappropriately activate pathways that promote the self-renewal of normal stem cells</one>.
+- For <one>divisional asymmetry</one>, which happens during <two>pre cell-division</two>, how is the cell fate determined? Via <one>asymmetric localization of cell fate determinants</one>.
+- For <one>asymmetric cell division</one> in <two>stem cells</two>, which two models can be distinguished? (1) <one>divisional asymmetry</one> (2) <one>environmental asymmetry</one>
+- The <one>epigenetic landscape</one> was coined by ... ? <one>Waddington</one>. URL: https://en.wikipedia.org/wiki/C._H._Waddington#Epigenetic_landscape []
+- Um <one>iPS-Zellen</one> zu induzieren verwendete man im Jahre 2012 welche vier wichtigen Transkriptionsfaktoren? (1) <one>OCT4</one> (2) <one>SOX2</one> (3) <one>c-MYC</one> (4) <one>KLF4</one>
+- Name a very unusual source for <one>human stem cells</one>. A: <one>Cadavers</one>.
+- <one>EC cells</one> are a type of <two>pluripotent stem cells</two> derived from ... ? <one>Teratocarcinoma</one>.
+- Give an example for <one>undifferentiated cells from the embryo</one>. A: <one>Embryonic stem cells</one>.
+- Name a <one>transcription factor</one> that is <two>essential for muscle differentiation</two>. A: <one>myoD</one>. []
+- If you get a <one>lung</one> from another patient who has been a heavy smoker, why may you very quickly die soon afterwards, due to cancer? Because there already were injured/cancerous cells in that smoking person; after transplantation you get a lot of drugs that inhibit the immune system, which is why cancer will spread more rapidly in the "new" transplanted person's body.
+- Give an example for a <one>unipotent</one> stem cell in the human body. A: The <one>muscle stem cells</one>.
+- Which human tissue may be a <one>true syncytium</one>? The <one>skeletal muscle</one>. These are a multinucleate cell which resulted from multiple cell fusions of uninuclear cells. []
+- Name two tissues in the human body that can regenerate regularly. A: (1) <one>blood</one> (2) <one>skin</one>
+- What determines specialization of cells? The <one>regulation of gene expression</one>.
+- Name two different strategies how a particular pattern of active and inactive genes can be transmitted to, and maintained by, daughter cells. A: (1) make use of chromatin structure as a memory system (2) make use of a protein, such as a transcription factor like the myoD protein
+- The <one>immediate environment</one> of a stem cell is called ... ? Its <one>niche</one>. []
+- <one>Mouse iPSCs</one> were generated by Shinya Yamanaka, using which 4 factors? (1) Oct4 (2) Klf4 (3) <one>Sox2</one> (4) <one>c-Myc</one>
+- There is a Yin/Yang situation in regards to cell division in general. When cells enter the final stages of differentation, what may be the Yang situation here? They lose their ability to proliferate.
+- How much of the weight of <one>bones in humans</one> is made up of <two>living cells</two>, in percent? About <one>15%</one>. []
+- Name the <one>two broad categories of smooth muscle cells</one>. A: (1) <one>unitary</one> (2) <one>multiunit</one>
+- How are the individual cells in a <one>cardiac muscle</one> called? <one>Cardiomyocytes</one>. []
+- <one>Which animals</one> are used in <three>stem cell research</three> in order to test human cancer? <one>Immunodeficient mice</one>. []
+- There is one tumor type that contains a mixture of differentiated cells. What is its name? <one>Teratocarcinoma</one>:
+- What is meant with the term <one>embryonal tumors</one>, in stem cell research? This refers to <one>tumors derived from embryonic cells</one>.
+- When we speak of a <one>stem cell</one>, we typically mean which stem cell? The <one>hematopoeitic stem cell</one>. []
+- In stem cell therapy: an alternative to <two>whole‐cell therapy</two> is to make use of ... ? <one>Exosomes</one>.
+- Name 4 different <one>cell sources</one> for tissue regeneration. A: (1) adipose tissue (2) umbilical cord (3) amniotic membrane (4) blood
+- There are <one>some stem cells</one> that do not undergo continuous division, but are kept in reserve to deal with tissue regeneration, when required. Give an example for this. A: The <one>muscle satellite cells</one>.
+- <one>Chondrocytes</one> were, in the year 1997, first transplanted utilizing a polymer-cell construct to produce tissue-engineered cartilage in the shape of a human ear, in which organism? In a mouse - the <one>ear on a mouse</one> project.
+- A <one>multiunit smooth muscle</one> can, for example, be found <two>where in the human body</two>? In the <one>iris of the human eye</one>. []
+- How many cells of the <one>bone marrow</one> are stem cells? <one>1</one> out of <two>50.000 to 100.000</two>. []
+- Hafner: Are <one>smooth muscles</one> striated? No, they are <one>non-striated</one>.
+- <two>Which filament</two> provides the backbone for <one>muscle contraction</one>? <one>Actin filaments</one>. []
+- <one>Myelin</one> is what kind of complex? It is a <one>protein-lipid complex</one>.
+- From <one>somatic cells</one> to "ES-like stem cells" via ... (one word only)? <two>Reprogramming</two>.
+- If we would have to list <two>a single gene</two>, which one would it be that would designate a cell to be a <one>stem cell</one>? The gene <one>ABCG2</one>/<one>Bcrp1</one>.
+- <one>Cells derived from stem cells</one> that proliferate for a limited number of cycles are called ... ? <one>Progenitor cells</one>. []
+- Give a specific example in <one>stem cell research</one> for treating medical conditions, aside from limb regeneration. A: The generation of pancreatic insulin-producing cells, in order to treat type I diabetes.
+- Give a specific example for a <one>macroglia</one> cell. A: The <one>Schwann cells</one>.
+- If we wish to destroy most of the hematopoietic cells, such as to treat leukemia, what could we do? We could apply a <one>large dose of x-rays</one>. []
+- <one>iPSCs</one> is short for ... ? <one>Induced pluripotent stem cells</one>. []
+- Name the four main families of cell adhesion molecules (move this to cellbiology once the stem-cell exam has been passed). A: (1) Integrins (2) Immunoglobulins (3) Cadherins (4) <one>Selectins</one>
+- Name <one>a common stem cell biomarker</one>, via the <two>CD nomenclature</two>. A: <one>CD34</one>. URL: https://en.wikipedia.org/wiki/CD34 []
+- Name a <two>limitation</two> of the potential of <one>embryonic stem cells</one>. A: They do not give rise to <one>extraembryonic tissue</one> such as those of the <two>placenta</two>.
+- The <one>parent science</one> of stem cell biology is ... ? <one>Developmental biology</one>. []
+- Can the <one>differentiation of vertebrate skeletal striated muscle</one> be studied in the cell culture? Yes. []
+- In mammals, what may be common to most cells, from a structural cell biology point of view? The <one>organelles</one>. []
+- Why is <one>the clinical application of iPS cells</one> <two>restricted</two>? Because of their <one>tumorigenic potential</one>. []
+- In mammals: which three muscle types can be distinguished? (1) skeletal muscle (2) smooth muscle (3) cardiac muscle []
+- Most of the key genes in development require <one>which general class of transcription factors</one> for their expression? <one>Activators</one>. []
+- There are two main types of glia cells in the human body. Which ones are these? (1) <one>microglia</one> (2) <one>macroglia</one>
+- The human <one>central nervous system</one> (CNS) contains about how many neurons? <one>10**11 (100 billion) neurons</one>.
+- Are <one>smooth muscles</one> organized as a syncytium? No - they exist as <one>individual cells</one>.
+- How are the cells in the hart called that <one>initiate action potentials</one>? <one>Pacemaker cells</one>.
+- Wie können wir den Begriff <one>progenitor cells</one> übersetzen? <one>Vorläufer Zellen</one>. []
+- <one>Skeletal muscles</one> show what kind of <two>coupling</two>? <one>Eexcitation-contraction coupling</one>.
+- Is <one>cell differentiation</one> reversible? In some cases it is; but in general it is not.
+- The human body has about <one>how many different cell types</one>? About <one>210</one>.
+- Name a cell surface glycoprotein, CD-designation, that can be found on <one>human hematopoietic stem cells</one> (HSCs). A: The cell surface glycoprotein <one>CD34</one>. []
+- Which cell is 'typical' among all cells in the body? This is a trick question - there is no universal representative cell that we could call 'typical'.
+- If <one>fibroblasts</one> receive <two>myoD</two>, what will happen? They will <one>develop into muscle cells</one>. []
+- <one>Fused myoblasts</one> are also called ... ? <one>Myotubes</one>. URL: https://en.wikipedia.org/wiki/Myogenesis []
+- Can <one>label‐retaining behavior</one> be considered to be a characteristic of stem cells? Yes. This can be used via <one>BrdU</one>.
+- What do we mean with the term <one>ES cells</one>? <one>Embryonic stem cells</one>. []
+- Name two cell types that can divide after differentation. A: (1) fibroblasts (2) liver cells
+- What do we mean with the term <one>potency</one>? This means to have <one>a high possibility</one> for differentiation into <two>different cell types</two>.
+- Which important property do stem cells have that other cells lack? They are all able to <one>divide asymmetrically</one>. []
+- A key member of the pluripotency group is <one>which POU‐domain transcription factor</one>? <one>Oct-4</one>. URL: https://de.wikipedia.org/wiki/Oct-4 []
+- A <one>stem cell</one> could become a stem cell, after a cell division, or it could become ... ? A <one>specialized cell</one>, such as a neuron.
+- <two>Which biomarker</two> could be used, to some extent, to assume that this may be <one>a stem cell marker</one>? The presence of <one>telomerase</one>.
+- <one>Self-renewing tissues in a mammal</one>: who is the <three>speed-champion</three> here, aka the fastest at it? The <one>gut</one>; or more accurately, the <two>lining of the small intestine</two>.
+- Give another name for the <one>inner cell mass</one>. A: <one>Embryoblast</one>.
+- For a cell: the first step in differentiation is ... ? For a cell to become committed - aka determine to becoming a particular cell type.
+- How do we call the cells that form <one>the intermediates</one> between stem cells and terminally differentiated cells? <one>Progenitor cells</one>.
+- <one>Mouse myoblast cells</one> in cell culture will continue to divide until what manual step can be taken? We can <one>remove growth factors</one>; then these myoblasts will no longer divide.
+- How do we call <one>the division-style of stem cells</one>? <one>Asymmetrical</one>. []
+- When was the <one>stem cell niche concept</one> first introduced? In <one>1978</one>. ULR: https://en.wikipedia.org/wiki/Stem-cell_niche []
+- Is there a gene product which is found in all stem cells and not in non‐stem cell? No. []
+- What is meant with the term <one>cell-replacement therapy</one>? This refers to <one>the restoration of tissue function by the introduction of new healthy cells</one>.
+- What is, sort of, <one>the opposite of cell differentiation</one>? <one>Transdifferentiation</one>.
+- Which <one>two types of pluripotent stem cells</one> exist? (1) The <one>embryonic stem cells</one> (<two>ESC</two>) (2) The <one>induced pluripotent stem cells</one> (<two>iPSC</two>)
+- Name the three main <one>potencies</one> of stem cells. A: (1) <one>pluripotency</one> (2) <one>multipotency</one> (3) <one>unipotency</one>
+- In stem cells: name four points that an Informed Consent Donation Form must include or must require, from the point of view of the <one>donor</one>. A: (1) the <two>donor</two> <one>must not be at high risk of transmitting infectious diseases</one> (2) the <two>donor</two> <one>must complete a medical evaluation questionnaire</one> (3) the <one>HLA type</one>, <one>blood group</one>, and IDM of the <two>donor</two> <one>must be made available to international registries and transplant centers</one> (4) the <one>risks of haematopoietic stem cell donation</one> must be explained and understood
+- In <one>stem cell terminology</one>: what comes before the <three>phenotypic modification</three>? <one>Transcriptional modification</one>.
+- <one>Stem cells</one> are roughly categorized into which 3 categories? (1) <one>ESCs</one>: <two>embryonic stem cells</two> (2) <one>MSCs</one>: <two>mesenchymal stem cells</two> (3) <one>iPSCs</one>: <two>induced pluripotent stem cells</two>
+- Where may we be most likely to find <one>megakaryocytes</one>? In the <one>bone marrow</one> (when these cells are mature). []
+- In stem cell science, name three <one>-potent</one> words, starting with the strongest one. A: (1) <one>totipotent</one> (2) <one>pluripotent</one> (3) <one>multipotent</one> []
+- Which person created <one>iPS</one> ("induced pluripotent stem") cells? <one>Shinya Yamanaka</one>.
+- <one>Cartilage tissue</one> consists of which cell type? <one>Chondrocytes</one>. URL: https://en.wikipedia.org/wiki/Chondrocyte []
+- Are <one>myoblasts</one> differentiated? By definition not really - they will divide upon stimulation via growth factors, but they are not yet differentiated (e. g. to be muscle cells).
+- <one>Mamallian striated skeletal muscle</one> originate from ... ? <one>Undifferentiated embryonic mesodermal cells</one>.
+- Give an example, in humans, for <one>pluripotent cells</one>. A: The <one>embryonic stem cells</one>.
+- Give a general <two>definition</two> of a <one>stem cell</one> that is the most characteristic one. A: Stemm cells are cells that show <one>self-renewal capacity</one>, that is, "infinite cellular division".
+- What cells stand for <one>multipotent MSCs</one>? These are <one>multipotent Mesenchymal stem cells</one>. []
+- How can we define <one>tissue engineering</one>? Tissue engineering refers to the use of a combination of cells, engineering and materials methods, and suitable biochemical and physico-chemical factors to improve or replace biological functions.
+- Give an example for an <one>unipotent stem cell</one>. A: The <one>muscle stem cells</one>. URL: https://www.nature.com/subjects/muscle-stem-cells []
+- Can <one>human stem cells</one> be recovered from cadavers? Yes - <one>up to 20h post mortem</one>.
+- <one>Transplantation of stem cell population</one>, may be either of ... which three possibilities? (1) autologous (2) syngeneic (3) <one>allogeneiuc</one>
+- What do we mean with a <one>tripotent stem cell</one>? One that <one>can give rise to three progeny cells</one>.
+- Is there <one>a typical cell in the human body</one>? Not really. []
+- Name an important biological limit in <one>tissue engineering</one>. A: For a tissue to grow beyond a certain size, new blood vessel supply is vital, as otherwise the tissue would become <one>hypoxic</one>.
+- In <one>stem cells</one>: what does <three>potency</three> mean? This refers to <one>the number of possible fates open to a cell</one>.
+- A molecular marker which is known to be required for stem cell function is <one>LGR5</one>. This is an accessory receptor for which signaling molecules? For the <one>Wnt family</one> of signaling molecules.
+- Give another name for <one>self-renewal capacity</one>. A: <one>Infinite cellular division</one>.
+- <one>Stem cells</one> give rise to? They give rise to <one>specialized cells</one>. []
+- <one>Pluripotent stem cells</one> may give rise to almost all cell types, except for ... ? The <one>trophectoderm of the placenta</one>.
+- In the bone marrow, we can find the <one>HSC cells</one>, the <one>Hematopoietic stem cells</one>. How many cells in the bone marrow are HSC cells? About <one>1</one> in <two>10.000</two>.
+- What are <one>transit amplifying cells</one>? These cells arise from the stem cells and divide a finite number of times until they become differentiated.
+- The abbreviation <one>HSCs</one> is short for ... ? <one>Hematopoietic stem cells</one>. []
+- Name <one>two important properties of ES cells</one>. A: (1) <one>rapid proliferation</one> (2) <one>pluripotency</one>
+- From a molecular biology point of view: how do pluripotent stem cells maintain their pluripotent state? They express an important network of transcription factors which are necessary for maintaining this state. 
+- <one>Stem cells</one> can do which two essential <three>cell-division types</three>? (1) <one>symmetric  cell division</one> (2) <one>asymmetric cell division</one> []
+- How many <one>different cell types</one> can we find in human adults? About <one>210</one>. []
+- What is the <one>key feature in cell differentiation</one>? The <one>pattern of gene activation</one>.
+- Which cells create the <one>bone matrix</one>? <one>Osteoblasts</one>. []
+- What do we mean with <one>potency</one> in stem cell technology? Potency specifies the "differentiation potential", which is the potential to differentiate into different cell types of the stem cell. Some stem cells have more abilities or possibilities for differentiation than others.
+- The most famous, and well-studied tissue‐specific stem cells are the ... ? The <one>hematopoietic system</one> aka the <two>blood‐forming</two> cells.
+- <one>Platelets</one> arise from which cell? <one>Megakaryocytes</one>. URL: https://en.wikipedia.org/wiki/Megakaryocyte []
+- Name a technique with which we could <one>isolate hematopoietic stem cells</one>. A: We could use <one>flow cytometry</one> - and specific (monoclonal) antibodies.
+- Differentiate between <one>autologous transplantation</one> and <one>allogeneic transplantation</one>. A: (1) <one>autologous</one> is when the donor is the same as the recipient. (2) <one>allogeneic</one> is when the donor is NOT the same as the recipient.
+- Name a <one>cell-based therapy</one> based on stem-cell research. A: <one>Matrix-associated chondrocyte implantation</one>.
+- Give another, fancier name for <one>stem cells</one>. A: <one>Miracle cells</one>.
+- <one>Oligopotent cells</one>: give a specific example for that. A: These cells can differentiate into only a few cells, such as <one>myeloid cells</one> or <one>lymphoid cells</one>.
+- Name the 3 major characteristics of the <one>adult stem cells</one>. A: (1) lifelong ability to self-renew (2) extensive proliferation (3) differentiation of progeny into multiple lineages

data/lib/studium/exam_topics/stickstofffixierung

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+# =========================================================================== #
+# === Stickstofffixierung
+#
+# This is also known as "nitrogen-fixation".
+# =========================================================================== #
+
+- <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.
+- Nenne <one>Input</one> und <one>Output</one> der <two>Nitrogenase</two>. A: <one>Input</one>: <two>N₂</two>, <one>Output</one>: <two>NH₄</two>.
+- Was enthält die <one>alternative Nitrogenase</one> anstatt <two>Molybdän</two>? <one>Vanadium</one>. []
+- <one>Nitrogenase</one> is sensitive to ... ? <one>O₂</one>.
+- <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>heterocysts</one> used by some <two>cyanobacteria</two> lose what upon becoming heterocysts? Their ability for photosynthetic capacity. []
+- The <one>nitrogen starvation sigma factor</one> is ... ? <one>sigma-54</one>. URL: https://www.nature.com/articles/nrmicro2058 []
+- <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.
+- 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
+- For <one>nitrogen fixation found in land plants</one>: name a bacterium that begins with the letter B and grows in nodules on these plants. A: <one>Bradyrhizobium japonicum</one>. URL: https://en.wikipedia.org/wiki/Bradyrhizobium_japonicum []
+- <one>Nitrogen fixation</one> requires how reduction cycles through nitrogenase? <one>Four</one>. []
+- <one>Heterocyst development</one> is directed by a complex genetic program induced by ... ? <one>Nitrogen starvation</one>. []
+- 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>Warum</one> ist die <two>ATP-Hydrolyse</two> wichtig für die Nitrogenase? Die <one>ATP-Hydrolyse</one> zwingt die Nitrogenase in eine energireiche Konformation, in der das Redoxpotenzial der elektronenübertragenden FeS-Zentren extrem negativ wird.
+- Do <one>trees</one> make use of nitrogen fixation via symbiosis? Yes, such as can seen in <one>alder trees</one>.
+- The <b>FeMo protein</b> binds 2 H⁺ and emits ... ? <one>H₂</one>.
+- Why is the nitrogenase extremely sensitive to oxygen? Because of the large reducing power needed to make NH4+. Thus, cells can fix nitrogen only in an anaerobic environment.
+- Was wird bei der <one>Stickstofffixierung</one> pro fixiertem <three>N₂</three> freigesetzt? <one>H₂</one>. []
+- <one>Industrial nitrogen</one> fixation uses ... ? The <one>Haber process</one>, also called <one>Haber-Bosch process</one>. URL: https://en.wikipedia.org/wiki/Haber_process []
+- <one>Which compounds</one> can <two>Nitrogenase</two> reduce? (1) <one>N₂</one> (2) <one>acetylene</one> []
+- One consequence of <one>nitrogenase structure</one> of nitrogen-fixing organisms is ... ? The nitrogenase <one>requires molybden</one> and so do the organisms that do fix nitrogen. Some alternative nitrogenases require vanadium instead of molybdenum, though, thus bypassing a need for molybdenum.
+- Nitrogenase typically contains the FeMo cluster. This cluster requires electrons delivered from another cluster, though. Which cluster is that? The P cluster (a Fe2S cluster) provides electrons to the FeMo cluster.
+- Why is photosynthesis turned off in heterocysts? Because these microorganisms wish to maintain anaerobic conditions in these heterocysts.
+- 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>)
+- The <one>nitrogenase</one> is protected via ... ? Name three different strategies employed here. A: Slime formation around cell, respiration, specialized cells (heterocysts) with thick cell walls in some Cyanobacteria.
+- Die meisten Nitrogenasen können welche Substanz reduzieren? <one>Acetylene</one>. []
+- 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>.
+- <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). []
+- 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>.
+- 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>? Rhizobien gehören zu den <one>Alphaproteobacteria</one>. URL: https://en.wikipedia.org/wiki/Alphaproteobacteria []
+- Die <one>Nitrogenase</one> braucht welchen Kofaktor? <one>Molybdän</one>. []
+- Why is the enzyme <one>nitrogenase</one> so sensitive towards oxygen? Because of the large reducing power needed to make NH4+.
+- <one>Stickstofffixierung</one> wurde beobachtet in einer <two>pH-Spanne</two> von ... bis ... ? Von <one>pH 2 bis pH 10</one>. []
+- Name <one>two different clusters</one> that can be found in the nitrogenase. A: (1) The <one>[4Fe-4S] cluster</one> (2) The <one>FeMo-co cluster</one>
+- The <one>first nitrogenase complex isolated</one> came from <i>Clostridium pasteruianum</i>, from the DuPont Laboratory, in which year? In <one>1960</one>. []
+- <one>Which gene product</one> is the <two>regulator of nodulation</two>? <one>nodD</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>Nitrogen fixation</one> works up towards a temperature of at the least ... n °C? <one>92°C</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 []
+- Alle <one>Nitrogen-fixierenden Organismen</one> müssen einen Mechanismus besitzen um die Konzentration an Sauerstoff niedrig zu halten. Warum? A: Weil das Enzym <one>Nitrogenase</one> <two>sehr sensitiv gegenüber Sauerstoff ist</two>. []
+- <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 []
+- 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>Nitrogenase</one> can be shut down not only by O₂, but also by which other molecule? <one>NH₃</one>. []
+- Do <one>nitrogenases</one> exist that <two>do not use molybdene</two> as cofactor? Yes, the so-called <one>alternative nitrogenases</one>. []
+- <one>Welche Person</one> entdeckte die ersten stickstofffixierenden Bakterien? <one>Martinus Beijerinck</one>. URL: https://de.wikipedia.org/wiki/Martinus_Willem_Beijerinck []
+- What may <one>inhibit nitrogen fixation</one>? <one>Oxygen</one>. []
+- 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. []
+- Die Nitrogenase besitzt den sogenannten P cluster, 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.
+- Are there <i>Archaea</i> that <two>can fix nitrogen</two>? <one>Yes</one> - for instance in <i>Methanococcus</i>. []
+- 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 []
+- <one>Which assay</one> can be used to detect nitrogen fixation? The <one>acetylene reduction assay</one>.
+- Die <one>Nitrogenase</one> (a nanomachine) verwendet was für einen Cofaktor? <one>Iron-Molybdenum</one> im Verhältnis 7:1, verbunden mit Schwefel-Atomen. []
+- Die <three>Nitrogenase</three> besteht aus <one>n Komponenten</one>? <one>Zwei</one>. []
+- Bei der Stickstoffixierung: <one>welche Aufgabe hat Komponente II der Nitrogenase</one>? Die Komponente II liefert die Elektronen.
+- 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>. []
+- <one>N₂ fixation</one> requires the enzyme ... ? <one>Nitrogenase</one>. URL: https://de.wikipedia.org/wiki/Nitrogenase []
+- Wird im Zuge der Stickstofffixierung <one>Hydrazin</one> gebildet? Ja. URL: https://de.wikipedia.org/wiki/Hydrazin []
+- Can <one>eukaryotes</one> fix nitrogen? No. []
+- Is <one>ATP</one> required for nitrogen fixation? <one>Yes it is</one>. The <two>dinitrogenase reductase</two> requires two ATP per cycle of electron transfer. []
+- <one>Welches Enzym</one> ist für <two>stickstoffoxidierende Mikroorganismen</two> extrem wichtig? Die <one>Nitrogenase</one>. URL: https://de.wikipedia.org/wiki/Nitrogenase []
+- The <one>NodD factor</one> for Legume-root symbiosis is induced by ...? <one>Flavonoids</one> extreted by plants.
+- <one>Nitrogen fixation by bacteria</one> typically creates which compound, as the <two>final product</two>? <one>NH₃</one>. []
+- Quelle der Reduktionskraft bei der <one>Stickstoffixierung</one>? <one>Reduziertes Ferredoxin</one>.
+- Definiere den Begriff <one>Stickstofffixierung</one>. A: Verwendung von <one>N₂</one> als <two>biosynthetischer Stickstoffquelle</two>.
+- <three>Welches Enzym</three> ist für die <one>Stickstofffixierung</one> am wichtigsten? Die <one>Nitrogenase</one>. URL: https://de.wikipedia.org/wiki/Nitrogenase
+- <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

@@ -0,0 +1,54 @@
+# =========================================================================== #
+# === 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"