studium 0.13.1

data/lib/studium/exam_topics/strukturbiologie

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+# =========================================================================== #
+# === Strukturbiologie
+#
+# Struktur und Funktion der Proteine. (folding tag)
+#
+# Struktur tag. Structure tag. Strukturbio tag. Protein Tag.
+# Struk tag. Röntgen tag, X-ray tag. Strukt tag.
+# Strukturbiologie tag.
+# =========================================================================== #
+
+- Name a hemoglobin-variant that begins with the letter C and was discovered in the year 2001. A: <one>Cytoglobin</one>. URL: https://en.wikipedia.org/wiki/Cytoglobin
+- Does the peptide bond make proteins more resistant to hydrolysis? Yes. Specifically the resonance structure that contributes to the planarity of peptide bonds makes these bonds more resistant to hydrolysis, and thus also the corresponding proteins.
+- Name <one>the two major contributors</one> to the energy difference between <two>the folded state</two> and <two>the denatured state</two>. A: (1) <one>enthalpy</one> (2) <one>entropy</one>
+- <one>How simple</one> is it to do unfolding/re-folding reactions, on <two>insulin</two>, in the laboratory? <one>Very difficult</one>; it gives <two>poor yields</two>. Many <one>incorrectly paired disulphide bridges</one> may form.
+- <one>How long</one> is a <two>beta sheet</two> typically, in <three>n aminoacids</three>? <one>3-10 aminoacids</one>. []
+- Wie sind <one>antiparallele Faltblattstränge</one> verbunden? Durch eine <one>Beta-Schleife</one>. []
+- <one>Bei welchem Protein</one> im menschlichen Körper kann der <two>allosterische Effekt</two> sehr gut beobachtet werden? Bei <one>Hämoglobin</one>. URL: https://de.wikipedia.org/wiki/H%C3%A4moglobin
+- A <one>membrane-spanning protein</one>, in its simplest form, has <two>how many and which segments</two>? <one>3</one>. (1) <two>one hydrophobic transmembrane segment</two> (2) <two>two hydrophobic regions</two> []
+- In folding of a protein: what do we mean with a <one>simple two-state equilibrium</one>? This refers to, for example, a simple unfolding when the native protein very quickly unfolds; and refolds also quickly. There is thus <one> no stable intermediate</one>.
+- Give an example for a <one>protein</one> that is able to form an <lightseagreen>infectious conformational state</lightseagreen>. A: <one>Prions</one>. URL: https://en.wikipedia.org/wiki/Prion []
+- How can we often call <one>non-oligomeres</one>? <one>Monomers</one>. []
+- Give an entertaining name for an <one>intrinsically unfolded</one> protein. A: A <one>floppy protein</one>. []
+- Wer oder was bestimmt die <one>Halbwertszeit eines Proteins</one>? Die <one>N-terminale Aminosäure</one>. []
+- Name a protein consisting largely of beta sheets, starting with the letter <one>p</one>. A: <one>Pepsin</one>. URL: https://en.wikipedia.org/wiki/Pepsin []
+- The <one>average length of an alpha-helix</one> is ...? About <one>10 amino acid residues</one>. []
+- Welche <three>3 Möglichkeiten</three> haben <one>Beta-Faltblätter</one> um geordnet zu werden? A: (1) <one>parallel</one> (2) <one>antiparallel</one> (3) <one>gemischt</one> []
+- <one>Welche Proteine</one> besitzen typischerweise <two>Disulfidbrücken</two>? Jene Proteine die das Endoplasmatische Retikulum durchschreiten - also vor allem <one>sekretorische Proteine</one>. []
+- What is <one>the basic paradigm of structural biology</one>? <one>Sequence → Structure → Function</one>. []
+- Between the <one>unfolded</one> and the <one>folded state</one> of proteins lies <two>which other state</two>? The <one>molten globule</one>. URL: https://de.wikipedia.org/wiki/Molten_Globule []
+- Give another name for <one>the fold space</one>. A: <one>Structure space</one>. []
+- In der Biochemie: was benötigen <one>parallele Beta-Stränge</one>? Eine <one>Überkreuzverbindung</one>. []
+- Molekulargewicht von <one>Myosin II</one>, in kDa? <one>500 kDa</one>. URL: https://de.wikipedia.org/wiki/Myosin_II []
+- <one>Polypeptide chains</one> with similar amino acid sequences fold to give ... ? <one>Similar 3D structures</one>. []
+- Give an example for <one>a globular, flexible molecule</one> that consists primarily of α-helices. A: <one>Myoglobin</one>. URL: https://en.wikipedia.org/wiki/Myoglobin []
+- Die Famile der <one>fork head HNF-3-related genes</one> kodiert für Transkriptionsfaktoren, der sogenannten <two>Fork head Box</two>. Diese Sequenz ist hoch konserviert, und umfasst in etwa wieviele Aminosäuren? Etwa <one>110 Aminosäuren</one>. Dieses Motiv wird mitunter auch <two>Winged-Helix Motiv</two> genannt.
+- Nenne ein Beispiel für eine relativ einfache <one>Supersekundärstruktur</one> in Proteinen. A: <one>Zwei Beta-Faltblätter</one>, die über eine Alpha-Helix miteinander verbunden sind.
+- The <one>F1-ATP Synthase component</one> has a diameter of ...? Of <one>9 nm</one>. []
+- Ist <one>Hämoglobin</one> ein <two>Homotetramer</two>? Nein. <two>Hämoglobin</two> ist ein <one>Heterotetramer</one>. URL: https://de.wikipedia.org/wiki/H%C3%A4moglobin#Struktur []
+- Angenommen ein Protein besitzt eine <one>aminoterminale Signalsequenz</one> - was können wir draus schliessen? Das dieses Protein zur <one>Sekretion</one> bestimmt sein mag. []
+- <one>What is responsible</one> for <two>the formation of alpha-helices and beta-sheets</two>? <one>Hydrogen bonding</one>. URL: https://www.britannica.com/science/hydrogen-bonding
+- What happens if we add an increasing amount of <one>GdmCl</one> (<cadetblue>guanidium chloride</cadetblue>) to proteins in solution? These <one>proteins will unfold</one>. URL: https://en.wikipedia.org/wiki/Guanidinium_chloride []
+- Give another name for the <one>superfamily of protein kinases</one>. A: The <one>kinome</one>. URL: https://en.wikipedia.org/wiki/Kinome []
+- Proteine wie zum Beispiel das <one>SSB-Protein</one> sind <two>"kooperativ"</two>. Was ist mit dieser Aussage gemeint? Das <one>ein gebundenes SSB-Protein</one> <two>die Bindung weiterer SSB-Proteine erleichtert</two>. []
+- Why would a cell require <one>rigid proteins</one>? In theory, <one>such proteins may be more stable</one> - but most proteins need some <two>structural flexibility</two>, so too rigid proteins are not a good idea from this point of view.
+- Is the analysis of charge and hydropathy sufficient to distinguish between structured and disordered proteins? In principle <one>yes</one>. []
+- In <one>structural biology</one>: why was the name TIM chosen for a <two>TIM barrel</two>? <one>TIM</one> stands for <two>triose phosphate isomerase</two>. URL: https://en.wikipedia.org/wiki/TIM_barrel
+- Name <one>two aminoacids</one> that are <two>effective chelators of metal ions</two>. A: (1) <one>Aspartic acid</one> (<two>aspartate</two>) (2) <one>Glutamic acid</one> (<two>glutamate</two>)
+- Nenne ein konkretes Beispiel für ein Protein das ein <one>four-helix bundle</one> inkludiert. A: <one>Cytochrom b562</one>. URL: https://de.wikipedia.org/wiki/Cytochrom_b []
+- Eine <one>Protein-Protein-Interaktion</one> ist <two>eine Wechselwirkung zwischen zwei oder mehreren Proteinen</two>. Sie beruhen überwiegend auf ... ? Auf <one>nicht-kovalenten Wechselwirkungen</one> - wie <two>van-der-Waals-Kräfte</two>, Wasserstoffbrückenbindungen sowie elektrostatischen Wechselwirkungen.
+- The <one>β-α-β motif</one> is frequently found in ... which proteins? In <one>ion channels</one>.
+- Nenne <one>zwei weitere Struktur-Elemente</one> in der Biochemie ausser dem <two>Beta-Faltblatt</two> und der <two>Alpha-Helix</two>. A: (1) <one>omega-loop</one> (2) <one>beta-turn</one> []
+- Ist die <one>Metallbindung</one> ein <two>strukturstabilisierender Faktor</two>? Ja - zum Beispiel <one>Zink</one> bei den <two>Zinkfingerproteinen</two>. []
+- In protein folding: <two>which state</two> occurs before the <one>final native state</one> of a folded protein? The <one>molten globule state</one>. URL: https://en.wikipedia.org/wiki/Molten_globule []
+- Wie können Sie, einfach und effizient, <two>experimentell feststellen</two>, <one>ob ein Protein in Lösung gefaltet vorliegt</one>? Mit Hilfe der <one>CD-Spektroskopie</one>. URL: https://de.wikipedia.org/wiki/Circulardichroismus []
+- Name the <one>three major advantages</one> of <two>NMR-spectroscopy</two> compared with X‐ray crystallography. A: (1) Protein structures in solution (2) Protein dynamics (3) Some proteins cannot be crystallized
+- Eine Aminosäure nimmt circa welches <one>Volumen</one> ein? <one>5 Angstrom x 5 Angstrom x 5 Angstrom</one>: also <two>125 Kubik-Angstrom</two>. []
+- The <one>alpha helix</one> is also called a classic ... ? <one>Pauling-Corey-Branson</one> alpha-helix. []
+- Die <one>durchschnittliche Proteingröße</one> liegt bei (<two>von-bis</two>) Aminosäuren? <one>200-400</one>. []
+- Name <one>two aminaocids</one> that show a <two>high propensity to form beat-sheets</two>. A: (1) <one>serine</one>   (<two>S</two>) (2) <one>threonine</one> (<two>T</two>) []
+- Can <one>a single aminoacid mutation</one> <two>in the core</two> cause the whole protein to <two>unfold</two>? Yes. []
+- Wie wird die <one>Bindungsstärke eines Proteins</one> genannt? <one>Affinität</one>. []
+- In einem <one>Ramachandran-Diagramm</one>: wo finden wir das <two>Beta-Faltblatt</two> allgemein eher? Beta-Faltblätter sind eher <one>links oben</one> im Ramachandran-Diagramm vorzufinden. []
+- Wenn wir <one>Calcium</one> (<two>²⁺</two>) mit <one>Zinn</one> (²⁺) vergleichen, die beide eine wichtige Rolle in der Strukturbiologie spielen mögen, <two>wer von den beiden besitzt einen kleineren Ionenradius</two>? <one>Zinn</one>.
+- Die <one>Chromodomäne</one>, eine Proteindomäne von etwa 40-50 Aminosäuren Länge, <two>wurde zuerst wo entdeckt</two>? Im <one>Drosophila melanogaster</one> Protein <two>Polycomb</two> (Pc). []
+- For <one>crystal structure</one>: we may modify <two>methionine</two> by adding which atom rather than its sulfur? <one>Selenium</one>. []
+- Was ist die <one>EF-Hand</one>? In der Proteinchemie, die Abfolge <one>Helix E</one>, <one>loop</one>, <one>Helix F</one>.
+- Nenne eine (für den Menschen) sehr wichtige Proteingruppe (ausgenommen Insulin), die <one>Disulfidbrücken</one> enthält. A: Die <one>Antikörper</one>. []
+- In amino acids, the <one>carboxyl groups</one> can be coupled to ...? <one>Amines</one>. []
+- The sidechains of two aminoacids with positive and negative charge can approach one another in space, to form ... ? <one>A salt bridge</one>. URL: https://en.wikipedia.org/wiki/Salt_bridge_(protein_and_supramolecular) []
+- A <one>single amino acid residue</one> spans ... <two>how many Angstrom</two>, roughly? About <one>3,8 Angstrom</one>. []
+- <one>A single amino acid residue</one> <two>spans about how many Angstroms</two>? About <one>3,8 Å</one>. []
+- Ist der <one>Ionenradius</one> von <two>Kalium</two> größer als der von <two>Calcium</two>? Ja. []
+- How do we call any region of a <one>protein surface</one> that allows interaction with another protein? A <one>binding site</one>. []
+- The unique biochemical fingerprint of proteins is ... ? Their <one>aminoacid sequence</one>. []
+- Which <one>physical force</one> or <one>physical factor</one> is highly responsible for <two>the specificity of interaction</two> between proteins? <one>Hydrogen bonds</one>. []
+- Im <one>Ramachandran-Plot</one> finden wir <two>links oben</two> ... ? Die <one>beta-sheets</one>. []
+- Nenne ein konkretes Beispiel für die Tertiärstruktur eines Proteins. A: Eine <one>vollständige Beta-Kette eines Hämoglobins</one>. []
+- In the <one>Protein Data Base</one> (<one>PDB</one>), as of the year <two>2017</two>: <three>how many percent of the structures registered there were solved by X-Ray analysis</three>, roughly? Almost <one>90%</one>. []
+- Is it easy to <one>refold insulin</one>? No. []
+- Die <one>Carbo-Anhydrase</one> verwendet welches Metall? <one>Zn</one><two>²⁺</two>.
+- <one>GFP</one> is <two>the representative of which new protein fold</two>? The <one>beta-can</one>. URL: http://www.cryst.bbk.ac.uk/PPS2/projects/jonda/structur.htm []
+- Hat <one>GFP</one> <two>beta-barrel(s)</two>? Ja. []
+- Kann <one>Zink</one> den <two>Schwefel von Methionin</two> an sich binden? Ja. []
+- Wie schwer ist ein Protein, das von <one>600 Nukleotiden</one> codiert wird? Dies sind <one>200 Aminosäuren</one>. Das durchschnittliche Gewicht einer Aminosäure in einem Polypeptid ist <two>110 Dalton</two>. Dies bedeutet auch <three>110 Gramm pro Mol</three>. Das mal 200, also 110 x 200 ergibt <four>22.000 Gramm pro Mol</four>. []
+- The ... of a protein is <one>the really stable form</one>. A: The <one>aggregate</one>. []
+- About <one>one third of all proteins</one> are ... ? <one>Metalloproteins</one>. []
+- <one>Wavelength</one> of X-rays, <two>in nm</two>? <one>0.1 nm</one> - thus very, very low. []
+- Was für ein <one>Profil</one> haben Proteine? Ein <one>Oberflächenprofil</one>. []
+- <one>Knowledge of structure</one> is also <two>knowledge of ... </two>? <one>Function</one>. []
+- <one>Disordered proteins</one> were shown to be <two>significantly depleted in which amino acid residues in particular</two>? In big <one>aromatic amino acid residues</one> such as <two>Tryptophan</two>, <two>Tyrosine</two> and <two>Phenylalanine</two>. []
+- In structural biology we can identify the so-called <one>β-Bends</one>. <two>Why was that name given to them</two>? <one>β-Bends</one> were given this name because <two>they often connect successive strands of antiparallel β-sheets</two>.
+- What is the native structure of intrinsically disordered proteins in general? They <one>do not adopt a (unique) native structure</one>. []
+- In structural biology: define the term <one>heteromultimeric</one>. A: These proteins contain <one>two ore more</one> <two>different polypeptide chains</two>. []
+- Give an example for a protein consisting predominantly of <one>alpha-helices</one>. A: <one>Myogloblin</one>. []
+- <one>When</one> were <two>x-rays</two> discovered? In <one>1901</one>, by <two>W. C. Röntgen</two>. []
+- When will a protein <one>NOT</one> have a <two>quaternary structure</two>? When it has <one>only one polypeptide chain</one>. []
+- Der <one>Ionenkanal MscL</one>, <two>ein Mechanosensor im Bakterium Mycobacterium tuberculosis</two>, besteht aus wievielen Untereinheiten? Aus <one>fünf</one> (<two>5</two>). []
+- Durchmesser einer <one>Alpha-Helix</one>, <two>in Angstrom</two>? <one>14 Angstrom</one>. []
+- In structure determination of proteins: the technique <one>ORD</one> is ... ? <one>Optical rotary dispersion</one>. URL: https://en.wikipedia.org/wiki/Optical_rotatory_dispersion []
+- <one>Proteins modified with lipids</one> are termed ... ? <one>Lipoproteins</one>. URL: https://en.wikipedia.org/wiki/Lipoprotein []
+- For the <one>phasing of protein crystals</one> in X-ray crystallyography, <two>what is absolutely required</two>? An <one>electron density map</one>.
+- <one>Welche Konformationen</one> kann eine <two>Peptidbindung</two> in einem Protein einnehmen? (1) <one>cis</one> (2) <one>trans</one> []
+- Andere Bezeichnung für die <one>Tertiärstruktur der Proteine</one>? <one>Domänen</one>. []
+- <one>The raw material of proteins</one> is/are ... ? <one>Amino acids</one>. []
+- Can <one>X-rays</one> be focused by lenses? No. []
+- The <one>proline helix</one> is a <two>left handed</two> or a <two>right handed</two> helix? It is <one>left handed</one>. []
+- Does <one>the hydrophobic effect</one> like to mix with water? No, of course not. []
+- <one>Misfolded proteins</one> tend to form ... ? <one>Aggregates</one>. []
+- What is <one>the underlying principle of molecular function</one>? <one>Structure</one>. []
+- <two>Beta Sheets</two> can be <one>antiparallel</one> and <one>parallel</one>. Which one of these two is more stable? <one>Antiparallel</one> is <two>more stable</two>. []
+- <one>Beta-Barrels</one> can have <two>which three major structures</two>? (1) <one>greek keys</one> (2) <one>jelly rolls</one> (3) <one>up-and-down barrel</one>
+- Mitglieder eines <one>Beta-Faltblatt</one> heissen (deutsche Bezeichnung) ... ? A: <one>Beta-Stränge</one>. []
+- The hydrophobic forces responsible for maintaining the 3D structures of proteins can be disrupted by ... what <one>kind of agents</one>? By <one>chaotropic agents</one>. URL: https://en.wikipedia.org/wiki/Chaotropic_agent []
+- How do we call the <one>small metal disk</one> in the middle of a X-Ray diffraction pattern? <one>Beam stop</one>. URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3150576/ []
+- Are <one>beta-sheets</one> <two>flat</two>? No - most beta-sheets are <one>twisted</one>. []
+- Die häufigste Form der <one>kovalenten Modifikation</one> von Proteinen ist ... ? Die <one>Phosphorylierung</one>. []
+- Der <one>durchschnittliche Stickstoffgehalt von Proteinen</one> beträgt <three>n%</three>? <one>16%</one>. []
+- Andere Bezeichnung für <one>Torsionswinkel</one>? <one>Diederwinkel</one>. URL: https://de.wikipedia.org/wiki/Diederwinkel []
+- In den Zink-Finger Proteinen (= Transkriptionsfaktor) wird <one>Zn</one><two>²⁺</two> durch <three>n Cysteine</three> komplexiert? <one>Vier</one> (<two>4</two>). []
+- Name a <one>biophysical method</one> with which we could <two>discover protein-protein interaction sites</two>. A: <one>NMR Mapping</one>. URL: https://www.nature.com/articles/nmeth0206-80 []
+- <two>Pro ATP</two> rotiert die <one>ATP-Synthase</one> <three>n°</three>? <one>120°</one>. URL: https://de.wikipedia.org/wiki/ATP-Synthase []
+- In <one>Ferritin</one> sind wie viel Prozent der Aminosäurereste zu <two>Alpha-Helices</two> gewunden? <one>75%</one>. URL: https://de.wikipedia.org/wiki/Ferritin []
+- Does <one>Ubiquitin</one> have <two>a highly hydrophobic core</two>? Yes. []
+- Can proteins <one>unfold upon cooling</one>? Yes - this phenomenon is known as <one>cold denaturation</one>. []
+- <one>Asparagine residues</one> are often found <two>where</two> in an <three>alpha-helix</three>? Near the <one>beginning</one> or the <one>end</one> of that alpha-helix. []
+- Does <one>protein folding</one> occur <two>spontaneously</two>? Yes. URL: https://en.wikipedia.org/wiki/Protein_folding []
+- <one>Warum</one> kann die Strukturbiologie kaum auf Einzelebene der Aminosäuren Vorhersagen treffen? Da selbst wenn wir zum Beispiel 2 Aminosäuren beschreiben können, die miteinander wechselwirken, wir eine unrealistische Annahme treffen, da ein Protein aus vielen Aminosäuren besteht, die miteinander in 3D sich gegenseitig beeinflussen können (+ Wassermoleküle in der Umgebung).
+- A protein contains <one>internal peptide bonds</one>, which <two>are formed during a condensation reaction</two> - thus, water is formed. <three>Who contributes the atoms in the H₂O molecule</three>? The <one>carboxyl group (COOH)</one> contributes a <two>H</two> and a <two>O</two>, and the amino group loses a N.
+- Give an example for a protein that consists of a <one>beta-barrel</one>. A: The <one>Porin proteins</one>. URL: https://en.wikipedia.org/wiki/Porin_(protein) []
+- If a <one>flavoprotein</one> is yellow, what do we know about it? That this flavoprotein must be in an <one>oxidized state</one>. []
+- How do we call the connections in a protein reached via <one>electrostatic interactions</one>. A: <one>Salt bridges</one>. []
+- Name <one>two intrinsic reasons</one> for what may complicate the folding process of proteins. A: (1) disulfide bridge: in particular when non-native disulfide bridges are possible (2) cis-trans isomerization of proline residues
+- <one>Valine</one> stiffens a main polypeptide chain similar to ...? <one>Isoleucine</one>. URL: https://en.wikipedia.org/wiki/Isoleucine []
+- Die <one>erste Röntgenstrukturanalyse bei einem Protein</one> überhaupt, erfolgte <two>an welchem Protein genau</two>? An <one>Myoglobin</one>. URL: https://de.wikipedia.org/wiki/Myoglobin []
+- Hat ein Protein einen <one>Schmelzpunkt</one> so deutet dies worauf hin? Das es in einer bestimmten 3D-Struktur vorliegt - also <one>nicht ungefaltet</one> vorliegen kann. []
+- Das <one>Ca-Bindungsmotiv</one> wird <two>von welcher Aminosäure bereitgestellt</two>? <one>Aspartat</one> (<two>D</two>). []
+- The <one>3.10 helix</one> has <two>n amino acids per turn</two>? <one>3</one>. URL: https://en.wikipedia.org/wiki/310_helix []
+- A <one>Ramachandran plot</one> displays all aminoacids? No - <two>two aminoacids can not be found there</two>, namely <one>glycine</one> and <one>proline</one> can not be found in a Ramachandran plot. []
+- Bei den photometrischen Proteinbestimmungsmethoden wird das Ergebnis mittels einer <one>Kalibrationskurve</one> ermittelt. Diese Kurve wird mit einem reinen Protein erstellt, sehr häufig <two>mit welchem Protein</two>? Mit <two>BSA</two> - bovines Serumalbumin (<one>bovine serum albumin</one>), eben aus dem Rind. URL: https://en.wikipedia.org/wiki/Bovine_serum_albumin []
+- The value of the <one>dielectric constant D</one> is important in structural biology. It has <two>a value of about 80 in water</two>, and ... in the hydrophobic core of a protein. A: About <one>3-5</one> <two>in the hydrophobic core of a protein</two>. []
+- <one>Wie</one> konnte man die Bindungslänge und den Bindungswinkel der Peptidbindung bestimmen? Mit Hilfe der <one>Röntgenstrukturanalyse</one>.
+- Ist eine <one>Transmembrandomäne</one> eher <two>hydrophil</two> oder eher <two>hydrophob</two>? <one>Transmembrandomänen</one> sind <two>eher hydrophob</two>. []
+- Je kleiner der <one>KD-Wert</one>, desto ... ist die <one>Affinität</one>? Desto <one>größer</one>/<one>höher</one>. []
+- Do <one>zink finger proteins</one> typically <two>require zink in order to fold</two>? Yes - normally this is the case. []
+- The <one>Protein Structure Continuum</one> may lead to <two>IDPs</two>. What does this abbreviation stand for? <one>IDPs</one> stands for <two>Intrinsically Disordered Proteins</two>. URL: https://en.wikipedia.org/wiki/Intrinsically_disordered_proteins []
+- Wirken <one>chaotrope Substanzen</one> denaturierend auf Proteine? Ja. URL: https://de.wikipedia.org/wiki/Chaotrope_Verbindung []
+- The <one>upper size limit of NMR</one> applied onto proteins is <two>about n aminoacids</two>? About <one>~350 aminoacids</one> (~40kDa).
+- Give an example for <one>a transport protein</one>. A: <one>Hemoglobin</one>. URL: https://en.wikipedia.org/wiki/Hemoglobin []
+- <one>Chaperone</one> gehören zu welcher <two>Proteinfamilie</two>? <two>Chaperone</two> gehören zu den <one>Hitzeschockproteinen</one>. []
+- In einem Protein: <one>parallele Stränge</one> benötigen was? Eine <one>Überkreuzverbindung</one>. []
+- Name the <one>three main methods for protein structure determination</one>. A: (1) <one>X-ray Crystallography</one> (2) <one>NMR Spectroscopy</one> (3) <one>Electron Microscopy</one> []
+- For structural biology it is useful to remember <one>the molecular mass of the average amino acid</one>, which is ... ? <one>100 Da</one>. []
+- Die <one>Alpha-Helix</one> wurde in welchem Jahr postuliert? <one>1951</one>. URL: https://de.wikipedia.org/wiki/%CE%91-Helix#Geschichte []
+- Do <one>alpha-helices</one> have a <lightseagreen>dipole</lightseagreen>? Yes. []
+- Name a protein with an <one>ATP-dependent protease activity</one>. A: The <one>RecA protein</one>. URL: https://en.wikipedia.org/wiki/RecA []
+- Kann der <one>Schwefel</one> <two>in einem Zinkfinger</two> chiral sein? Ja. []
+- <two>Welche Formen</two> können <one>Beta-Faltblätter</one> einnehmen? A: <one>Parallel</one>, <one>antiparallel</one> und eine <one>Mischform</one> davon. []
+- A <one>crystal</one> consists of ...? <one>Identical unit cells</one>. URL: https://en.wikipedia.org/wiki/Crystal []
+- In structural biology: is the <one>left handed helix</one> more common than the <one>right handed helix</one>? <two>No</two> - <one>the right handed helix is more common</one>. []
+- Das <one>Beta-Haarnadelschleifenmotif</one>: <two>nenne ein Beispiel eines Proteins, das dieses Motif besitzt</two>. A: <one>Bovine Trypsin Inhibitor</one>.
+- Die <one>CD-Spektroskopie</one> funktioniert bei welcher Aminosäure nicht? <one>Glycin</one>, da diese Aminosäure <two>nicht chiral</two> ist. []
+- Im <one>Ramachandran-Plot</one> finden wir <two>links unten</two> ... ? Die <one>Alpha-Helix</one>. URL: https://de.wikipedia.org/wiki/Ramachandran-Plot []
+- Es gibt das Strukturmotiv <one>EF-Hand</one>, das man als eine menschliche Hand zeichnen mag. <two>Wieviele Finger müssen wir hierbei verwenden</two>? <one>3</one>. URL: https://en.wikipedia.org/wiki/EF_hand []
+- If we are to <one>increase the negative surface charge</one>, would this <two>affect protein solubility</two>? If so, how? A: An increase in the negative surface charge correlates strongly with <one>increased protein solubility</one>. []
+- <one>G-Proteine</one> werden auch <two>7-Transmembran-Rezeptoren</two> genannt. Warum? Da sie <one>7 Alpha-Helices</one> besitzen.
+- A <one>sticky patch</one> on the surface of a molecule can create problems. <two>Give a specific example to reinforce this statement</two>. A: <two>Hemoglobin</two>, in the sickle-cell mutation, has such a <one>sticky patch on the surface</one>. In this mutation, a charged glutamic acid is replaced with the non-polar valine, which causes this <one>sticky patch</one> situation. []
+- Say that a researcher employs <one>Dithiothreitol</one>. <two>What will the effect be upon proteins</two>? <one>Dithiothreitol</one> is a <two>thiol reagent</two> that <three>will dissolve disulfide bonds</three> between cysteine amino acids.
+- Wie nennt man Proteine mit <one>mindestens zwei Polypeptidketten</one>? <one>Multimere Proteine</one>. []
+- Can the <one>peptide bond</one> be involved in <two>hydrogen bonds</two>? Yes. See the stabilization in <one>α-helices</one> and in <one>β-sheets</one>.
+- Durchmesser der <one>Alpha-Helix</one>, in Angstrom? <one>14 Angstrom</one>. []
+- <one>The first resolved crystal structure of a protein</one> was <two>hemoglobin</two>, in the year ... ? <one>1959</one>. URL: https://en.wikipedia.org/wiki/Hemoglobin []
+- Welche <one>Aminosäure</one> ist meistens bei einer <two>cis-Konformation der Peptidbindung</two> zu finden? <one>Prolin</one>. []
+- Das <one>BiP</one> (<two>Binding Protein</two>) ist <three>worin</three> eine Schlüsselkomponente? <one>BiP</one> ist eine Schlüsselkomponente in der <two>Unfolded protein response</two>. URL: https://en.wikipedia.org/wiki/Unfolded_protein_response []
+- One of <one>the most fundamental question</one> about a protein is ... ? Its (natural) <one>function in a cell</one>. []
+- <one>Lipocalins</one> are an <two>eight-stranded barrel</two>. They can bind ... ? <one>Retinol</one>. URL: https://en.wikipedia.org/wiki/Lipocalin []
+- Verschiedene Aminosäuren haben eine <one>unterschiedliche Neigung</one> zur <two>Alpha-Helix Strukturbildung</two>. <three>Welche fünf Aminosäuren sind besonders gute Alpha-Helix Strukturbildner</three>? <one>MALEK</one> (1) <two>Methionin</two> (2) <two>Alanin</two> (3) <two>Leucin</two> (4) <two>Glutamat</two> (5) <two>Lysine</two>
+- Compare <one>the average length of soluble proteins</one> to <two>membrane-bound proteins</two>. A: <one>Soluble proteins</one> <two>tend to be shorter</two> than <one>membrane-bound proteins</one>.
+- Ist für die Synthese einer Peptidbindung ein <one>hoher Energieaufwand</one> notwendig? Ja. []
+- <one>Until which year</one> was it not possible to deduce the 3D structure of a large protein? Until <one>1960</one>. []
+- How do we call <one>identical units</one> in a polypeptide chain? <one>Protomers</one>. URL: https://en.wikipedia.org/wiki/Protomer []
+- The energy of (electrostatic) interaction is described by <one>which law</one>? By the <one>law of Coulomb</one>. URL: https://en.wikipedia.org/wiki/Coulomb%27s_law []
+- Was wird als <one>Apoprotein</one> bezeichnet? Der Teil eines Proteins, der nur aus Aminosäuren besteht. []
+- Das <one>26S-Proteasom</one> ist ein Proteinkomplex, der <two>wie groß</two> ist (in kDa)? <one>1.700 kDa</one> (=<two>26S-Proteasom</two>). []
+- Das <one>Experiment von Anfinsen</one>, 1973, war in der Biochemie sehr wichtig. Als Substrat wurde <two>RNase A</two> verwendet. Was konnte man dank dieses Experiments zeigen? Die <one>RNase A</one> konnte durch <two>Urea</two> und <two>β-Mercaptoethanol</two> denaturiert werden. Danach auch wieder renaturiert, und die volle katalytische Aktivität wurde wieder gewonnen. Das Experiment war wichtig da man zeigen konnte, das die Information für die katalytische Tätigkeit alleine in der Abfolge der Aminosäuren begründet liegt. Zudem demonstrierte man damit auch die Wichtigkeit von <one>spontaneous folding</one>.
+- Können wir <one>CD-Spektren</one> verwenden um <two>Cyclopeptide</two> zu unterscheiden? Ja. []
+- Give another description for the <one>molten globule</one>. A: The <one>partially structured state</one>. URL: https://en.wikipedia.org/wiki/Molten_globule []
+- Preparing a sample for protein analysis via <one>imidazole</one> is difficult, as <one>imidazole</one> can overwhelm the spectrum <two>below ... which nm wavelength</two>? <one>220 nm</one>. []
+- <one>Alpha-Helices</one> contain <two>n amino acids per turn</two>, by default? <one>3.6</one>. []
+- Haemogoblin <one>Hbf</one> ... why the <peru>f</peru> there? <one>f ... fetal</one>. []
+- Proteins may show <one>a structure-... relationship</one>. A: A <one>structure-function relationship</one>. []
+- <one>Proteins may have stretches of disorder</one>, in their 3D shape. Compare eukaryotes to prokaryotes here: <two>who of these two groups has more disorder in their proteins</two>, in general? <one>Eukaryotic proteins show more disorder</one>. This may be due to the consequence of an increased need for cell signaling and regulation.
+- In <one>X-ray crystallography</one>: what kind of <lightseagreen>maps</lightseagreen> do we generate? We generate <one>electron density maps</one>. URL: https://dictionary.iucr.org/Electron_density_map []
+- <one>Albumin</one> ist wie gross (<two>von-bis</two>)? <one>65-70 kDa</one>. URL: https://de.wikipedia.org/wiki/Albumine []
+- Nenne drei Vorteile der <one>CD-Spektroskopie</one> (<one>Circulardichroismus</one>) gegenüber der <two>NMR</two>. A: (1) die <one>CD-Spektroskopie benötigt weniger Probenmaterial</one> (2) die <one>CD-Spektroskopie ist schneller</one> (3) die <one>CD-Spektroskopie ist weniger arbeitsintensiv</one>
+- Give an example for <one>a supersecondary (supercoiled) structure in the human body</one>. A: <one>Collagen</one>. URL: https://en.wikipedia.org/wiki/Collagen []
+- Gibt es Proteine ohne 3D-Struktur? <one>Strenggenommen eigentlich nein</one> - aber allgemein nennen wir eben entfaltete Proteine <two>unfolded</two>. []
+- Which of the following properties of a protein is <one>the least likely</one> to be affected by changes in pH? Pick one from: <two>Secondary structure</two>, <two>Net charge</two>, <two>Primary structure</two> or <two>Tertiary structure</two>. A: <one>Primary structure</one>. []
+- Does the <one>alpha-helix</one> have a <three>dipole moment</three>? Yes it does. []
+- Andere Bezeichnung für <one>fertig gefaltete Untereinheiten</one>? <one>Protomere</one>. URL: https://www.pschyrembel.de/Protomer/H008U []
+- Die <one>2D-Kristallisation von Proteinen</one> erfolgt <two>besonders gut bei welchen Proteinen</two>? Bei <one>Membranproteine</one>. []
+- Name a protein that is known to form, or be involved in, inter-species, <one>nano-wire</one>-like connections up to 1000 nm. A: <one>Cytochrome c</one>. []
+- In der schematischen Darstellung der <one>Beta-Stränge</one> zeigen die Pfeilende worauf? Auf das <one>carboxyterminale Ende</one>. []
+- Weisen <one>Beta-Faltblätter</one> eine <two>Polarität</two> auf? Nein. URL: https://de.wikipedia.org/wiki/%CE%92-Faltblatt []
+- Welche <one>Ladung</one> tragen die beiden Termini eines Proteins bei neutralem pH? Beide sind geladen, als <one>NH₃⁺</one> und <one>COO⁻</one>. []
+- <one>Lysine</one> has <two>how many different rotamers</two>? <one>81</one> (<two>3⁴</two>). []
+- Das erste Protein, dessen <one>atomare Struktur</one> aufgeklärt werden konnte, war ... ? A: <one>Myoglobin</one>. URL: https://de.wikipedia.org/wiki/Myoglobin []
+- What is the job of the <one>Wiggler</one> in a synchroton? The <two>wiggler</two> <one>increases the intensity of the beam</one>. (Mnemonic: <three>to wiggle the intensity of the beam</three>.)
+- Name the three main methods for <one>structure determination in protein research</one>. A: (1) <one>X-ray crystallography</one> (2) <one>NMR spectroscopy</one> (3) <one>electron microscopy</one>
+- One of the fastest proteins in regards to its own folding is ... ? <one>Ubiquitin</one>. URL: https://de.wikipedia.org/wiki/Ubiquitin []
+- Warum das <one>Beta</one> in Beta-Faltblatt? Da die <one>Alpha-Helix</one> zuerst gefunden wurde; so erschien es logisch das man Beta einfach Beta nennt. []
+- <one>Wavelength of X rays</one> in Angstrom, from-to? From about <one>0.5 Angstrom</one> up to <one>1.5 Angstrom</one>. URL: https://en.wikipedia.org/wiki/X-ray []
+- Does the <one>F1 ATPase</one> also <two>work in reverse</two>? <one>Yes</one> - <two>the ATPase can work in reverse</two> as well. []
+- Die <one>Beta-Faltblattstrukturen</one> <two>in globulären Proteinen</two> sind rechtsgängig oder linksgängig? Sie sind <one>ausnahmslos rechtsgängig</one>. []
+- What is <one>more stable</one>: <two>parallel</two> or <two>anti-parallel</two> Beta sheets? <one>Anti-parallel Beta sheets</one> are more stable. []
+- Is <one>geometry</one> important for <two>hydrogen bonds</two>? <one>Yes</one>. []
+- In <one>structural biology</one>, name the three core aspects to give a <two>comprehensive picture of proteins</two>. A: (1) <one>structure</one> (2) <one>thermodynamics</one> (3) <one>kinetics</one>
+- <one>Cytochrom-c-Proteine</one> besitzen welche Aminosäuren-Signatur, das Erkennungsmotiv dieser Proteingruppe? <one>CXXCH</one>. URL: https://en.wikipedia.org/wiki/Cytochrome_c#Structure []
+- Proteins have a ... <one>landscape</one>. A: An <one>energy landscape</one>. []
+- <two>Wann</two> wurde das <one>Friedel law</one> etabliert? Im Jahre <one>1913</one>. []
+- Can <three>circular dichroism</three> be used to <one>study protein interactions</one>? Yes. []
+- <one>Ganghöhe</one> der Alpha-Helix? Die Alpha-Helix besitzt eine Ganghöhe von <one>0.54 nm</one>. []
+- Warum ist der <one>Hydropathy-Index</one> wichtig? Weil man damit Vorhersagen kann <lightgreen>wo</lightgreen> eine Aminosäure zu finden ist. In einem Protein sind <one>hydrophobe Aminosäuren</one> meistens innen vorzufinden, <one>hydrophile Aminosäuren</one> sind aussen.
+- The <one>interior of a protein</one> is ...? <mediumseagreen>Hydrophobic</mediumseagreen>: proteins contain a <one>hydrophobic core</one>. []
+- <one>When</one> was the <two>Levinthal's paradox</two> suggested? In <one>1969</one>. URL: https://en.wikipedia.org/wiki/Levinthal%27s_paradox
+- Die <one>dreidimensionale Faltung der Proteine</one> folgt den <two>Gesetzen der ...</two>? <one>Thermodynamik</one>. []
+- Are <one>molten globules</one> <two>more accessible to proteolysis</two>? Yes. []
+- If we see <one>a protein with a SH2 domain</one>, what can we assume about that protein? That <one>this protein can bind to phosphotyrosines</one>. []
+- <one>Proteins</one> in general adopt which structure? The structure that <one>minimizes free energy</one>.
+- What is meant with the term <one>protein space</one>? This refers to <one>all possible proteins</one> - <two>an infinite space for the chemical space</two>, which is at the very least larger than protein space.
+- <one>Hsp70</one> bindet an ... <two>welche Bereiche eines ungefalteten Proteins</two>? An <one>hydrophobe Segmente</one>. URL: https://en.wikipedia.org/wiki/Hsp70 []
+- Können <one>gasförmige Moleküle</one> <two>Liganden für Proteine</two> sein? Ja. []
+- Name a <one>competitive inhibitor</one> that can <two>inhibit many serine proteases</two>. A: <one>Aprotinin</one>. URL: https://en.wikipedia.org/wiki/Aprotinin []
+- <two>How many proteins</two>, that is, <one>individual protein molecules</one>, can we find in an average mammalian cell? About <one>10 billion individual proteins</one>. []
+- <one>Dr. Michael Rossmann</one> is famous in <two>structural biology</two> for ...? Discovering the <one>Rossmann fold</one>. URL: https://en.wikipedia.org/wiki/Rossmann_fold []
+- Give another term for <one>angle pairs</one> of <two>phi</two> and <two>psi</two> in structural biology. A: <one>Ramachandran plot</one>. []
+- <one>Membrane proteins</one> typically - <two>at the least in eukaryotes</two> - <three>constitute n% of proteins encoded by whole genomes</three>? About <one>~30% of proteins</one>. []
+- When we compare two different proteins to one another, through <one>percent identity</one>: can the percent identity be <two>zero</two>? <one>No</one> - <two>proteins always have something in common</two>. []
+- Give another term for <one>global prediction of all protein-protein interactions</one>. A: The <one>Interactome</one>. URL: https://en.wikipedia.org/wiki/Interactome []
+- Ändert <one>Calmodulin</one> seine 3D-Struktur wenn es <mediumturquoise>Calmodulin</mediumturquoise> gebunden hat? Ja. URL: https://de.wikipedia.org/wiki/Calmodulin []
+- <one>CD-Spektroskopie</one>: wofür steht hier die Abkürzung <one>CD</one>? <one>Circulardichroismus</one>. URL: https://de.wikipedia.org/wiki/Circulardichroismus []
+- <one>Natural proteins fold spontaneously</one> to form unique, native structures. <two>How can this work</two>? The polypeptide chain is flexible. This allows these proteins to assume many different spatial conformations. At equilibrium the protein will adopt the native state.
+- Proteine bestehen aus Polypeptiden die eine <one>main chain</one> haben. <two>Verwende ein anderes Wort hierzu</two>. A: <one>Backbone</one>. []
+- Why can we not use <one>imidazole</one> in <two>protein spectroscopy</two>? Because <one>imidazole overwhelms the spectrum from then on</one>. []
+- Deutsche Bezeichnung für die <one>X-ray white radiation</one>? Dies bezeichnet die <one>Bremsstrahlung</one>. URL: https://de.wikipedia.org/wiki/Bremsstrahlung []
+- <two>Wo</two> (in einem Protein) findet man <one>phosphorylation sites</one>? Auf der <one>Oberfläche eines Proteins</one>. []
+- <two>Welche Person</two> schlug das <one>ribbon-Modell</one> für Proteine vor? <one>Jane Richardson</one>. URL: https://en.wikipedia.org/wiki/Jane_S._Richardson []
+- Ist die <one>Alpha-Helix</one> rechts- oder linksgängig? Sie ist <one>rechtsgängig</one>. []
+- In order to <two>crystallize</two> <one>problematic proteins</one>, <three>what kind of optimization</three> may we have to do in the lab usually? <one>Buffer optimization</one>. []
+- Die <one>relative Molekülmasse</one> eines Proteins (Mr) ist ... ? <one>38.000</one>. []
+- <two>Where</two> in the Ramachandran Plot can we find <one>left handed alpha-helices</one>? In the <one>upper right quadrant</one>. URL: https://en.wikipedia.org/wiki/Ramachandran_plot []
+- Woraus wird <one>die Tertiärstruktur von Proteinen</one> gebildet? Aus <one>Domänen</one>. []
+- Ein typisches <one>Beta-Faltblatt</one> enthält (von-bis) Beta-Stränge? Ein typisches Beta-Faltblatt besteht aus <one>2-15</one> einzelnen Beta-Strängen. []
+- Name a <one>major protein structure classification scheme</one>. A: <one>SCOP</one> (<two>Structural Classification of Proteins</two>). URL: https://scop.mrc-lmb.cam.ac.uk/ []
+- How is the <one>winged HTH domain</one> different from the (regular) <two>HTH domain</two>? The <one>winged HTH domain</one> has a longer turn, e. g. the <two>winged turn</two>, which is 10 aminoacids in length.
+- Are <one>aminoacids</one> <two>anisotropic compounds</two>? <one>Yes</one>. []
+- Die <one>2D-Kristallisation von Proteinen</one> ist besonders günstig für ... ? <one>Membranproteine</one>. []
+- If we have <one>an insoluble protein</one>, what could we do in the laboratory to make it more soluble? We could <one>attach SUMO to it</one>. <two>Ubiquitin-like proteins tend to fold very quickly in general</two>. []
+- The <one>average weight of an aminoacid</one> bound in a protein is ... ? <one>110 Dalton</one>. []
+- Give the mnemonic for <one>the trend of hydrophobicity parameters</one> for the L-aminoacids. A: F,(L,I),(Y,W),V,M,P,C,A,G,T,S,K,Q,N,H,D,E,R. Also, Phenomenäle Läuse der Isolde Yagen wilden Valentin.
+- Name one big advantage that <one>X-Ray</one> has over <one>NMR</one>. A: <one>X-Ray has no size limitation</one> in regards to the structure to be studied.
+- Say that <one>we want to disorder proteins by changing just one amino acid only</one>. <two>Which amino acid should we choose for this</two>? <two>Cysteine</two>. <two>Cysteine</two> is crucial, as it has a significant contribution to the protein conformation stability via <one>disulfide bond formation</one>. It also is involved in coordination of different prosthetic groups.
+- The <one>ends of alpha helices</one> can be found <two>where in a protein</two>? The <one>ends are</one> <two>polar</two>, and thus almost always on the <one>surface of protein molecules</one>.
+- Give a specific example for a protein that consists of lots of <one>alpha-helices</one>. A: <one>Myoglobin</one>. URL: https://en.wikipedia.org/wiki/Myoglobin
+- <two>Wann</two> wurde die <one>Alpha-Helix</one> vorgeschlagen? Im Jahre <one>1951</one>. URL: https://en.wikipedia.org/wiki/Alpha_helix#Discovery
+- Name <one>an important reason</one> as to why we <two>attempt to determine protein structures through high-throughput methods</two>. A: <one>Lower cost</one> due to <two>automation</two>.
+- <one>NMR analysis</one> works up to a protein size of n Daltons? Up to <one>100.000 Daltons</one>.
+- If we conclude that <one>two proteins are homologouos</one>, what else can we conclude from that statement, if it is true? That <one>their genes</one> must have evolved from a <two>common ancestral gene</two>.
+- Länge in der <one>Alpha-Helix</one> pro Aminosäure, <two>in nm</two>? <one>0.16 nm</one>.
+- In structural biology: in general the <one>X-ray method</one> is much better than the <one>NMR method</one>. One difficulty is to obtain the crystals, but <two>name an area where the NMR in particular excels</two>. A: <one>NMR</one> can be used to study <two>protein dynamics</two>.
+- Bei dem Einsatz von NMR zwecks Untersuchung der Proteine wird mitunter auch <one>NOE</one> (<two>Nuclear Overhauser Enhancement</two>) verwendet. Dies liefert uns welche Information zusätzlich? <one>NOE</one> liefert uns <two>zusätzliche Rauminformation</two>.
+- Give <one>seven general examples</one>/<one>reasons</one> as to the different functions of proteins. A: (1) structural proteins (2) enzymes (3) antibodies (4) regulatory proteins (5) sensors (6) <one>transporters</one> (7) <one>transducers</one>
+- In the <one>core</one> of <two>a typical globular protein</two>: <three>which factor is the most important one that stabilizes the core</three>? The <one>van-der-Waals force</one>.
+- Give two different reasons why we may wish to employ <one>X-ray</one> on protein crystals. A: (1) <one>design novel drugs</one> that target a particular protein (2) rationally engineer an enzyme for a specific industrial process
+- <one>Tryptophan</one> is often found where exactly on a given protein? <one>In the core</one> (aka center), primarily <two>due to its bulky shape</two> and secondarily due to its hydrophobicity.
+- <one>How a protein folds up into its native shape</one> not only dictates how the protein works, but is also important because ... ? Because that protein may interact with other entities (aka other proteins), and thus may have an important biological role in the cellular context.
+- <one>Wasserstoffbrücken</one> entstehen generell zwischen ...? (1) <one>Wasserstoff</one> und <two>Sauerstoff</two> (<two>O</two>) (2) <one>Wasserstoff</one> und <two>Stickstoff</two> (<two>N</two>)
+- <one>Wann</one> wurde die <two>Struktur von Lysozym</two> aufgeklärt? Im Jahre <one>1965</one>. URL: https://de.wikipedia.org/wiki/Lysozym#Geschichte
+- Nenne ein sehr häufiges Protein, das weitgehend aus <one>Alpha-Helices</one> besteht. A: <one>Hämoglobin</one>. URL: https://en.wikipedia.org/wiki/Alpha_helix#Functional_roles
+- <one>Which aminoacid</one> is <two>a fairly infrequently substituted residue</two>? <one>Cysteine</one>. Often substitution of cysteine with other residues abolishes the enzymatic activity, or destabilizes the protein structure, which may have a similar effect.
+- <one>Wovon</one> ist das Auflösungsvermögen einer <two>Röntgenanalyse</two> primär abhängig? Von der <one>Qualität des Kristalls</one>.
+- Was meinen wir mit <one>exozyklisch</one>? Dies ist <one>nicht im Ring</one>, zum Beispiel bei RNA, das C5'-Atom.
+- The <one>helix-turn-helix motif</one> is a functional motif that is often found in proteins that bind to DNA minor and major grooves, as well as proteins that <two>bind which metal</two>? <one>Calcium</one> - thus, in <two>calcium-binding proteins</two>.
+- What does the <one>Anfinsen dogma</one> state? <one>Protein folding occurs in self-assembly</one>. In other words, the peptide sequence contains the whole information for its assembly.
+- A <one>FRET signal</one> provides information about distances in the order of ... Å? About <one>10 Å to 100 Å</one>.
+- Anderer Begriff für <one>Tertiärstrukturen</one>? Möglicher <one>Endzustand eines Proteins</one>.
+- Wenn ein <one>Anion</one> in einem Protein stabiler wird, <two>wie ändert sich die Säurestärke</two>? Die <one>Säurestärke steigt</one>.
+- Welche <one>drei Komponenten</one> werden für eine <two>röntgenkristallographische Analyse</two> benötigt? (1) einen <one>Detektor</one> (2) ein <one>Proteinkristall</one> (3) <one>eine Quelle für Röntgenstrahlen</one>
+- Nenne <one>die drei wichtigsten Sekundärstrukturelemente von Proteinen</one>. A: (1) <one>alpha-Helix</one> (2) <one>beta-Faltblatt</one> (3) <one>beta-Schleife</one>
+- What can we consider to be <one>the building blocks of protein structure</one>? The <one>peptide units</one>.
+- In general: what is meant with <one>the hydrophobic effect</one>? The hydrophobic effect generally refers to the low solubility of hydrophobic compounds in water. These are <one>apolar</one> compounds. 
+- The rarer a protein-coding variant is (for a given gene), the more likely it is to represent ... what kind of change? a <one>non-conservative amino acid change</one>.
+- Name <one>two functionally important areas of proteins</one> in general. A: (1) <one>ligand-binding   sites</one> (2) <one>enzymatic active sites</one>
+- Können wir aus <one>Proteinstrukturen</one> auf <two>Liganden</two> ableiten? Ja, zum Teil: <one>Ähnliche Proteinstrukturen</one> bedeuten oft <two>ähnliche Liganden</two>.
+- Give an example of <one>where</one> we can find the <two>greek key motif</two>, a protein example. A: In the <one>Staphylococcus nuclease</one>. URL: https://en.wikipedia.org/wiki/Greek_key
+- We have the <one>Nm nomenclature for helices</one>. What does the <two>N</two> stand for, here? <two>N</two> refers to the <one>number of repeating units per turn</one>.
+- Is the <one>amide linkage</one> (of the peptide bond) <two>important for protein stability</two>? Yes. The amide linkage is very important for the three-dimensional structure of peptides and proteins.
+- Name <one>a substance</one> that <two>can be used to disrupt disulfide bonds of a protein</two>. A: <one>β-mercaptoethanol</one>.
+- <one>Proteine variieren sehr stark in der Größe</one>, <two>von nDa bis zu nDa</two>? Von <one>5_000 Da</one> bis zu <one>3_000_000 Da</one>.
+- Name <one>the three most common obstacles to correct folding</one>. A: (1) aggregation of the intermediate through exposed hydrophobic groups (2) <one>formation of incorrect disulfide bonds</one> (3) isomerization of proline residues
+- In structural biology: <one>an essential increase in the hydrodynamic volume</one> is associated with ... ? With <one>the unfolding of a protein molecule</one>.
+- <one>Calmodulin</one> can bind 4x Ca²⁺, which will cause Calmodulin to undergo a conformational change. Which structural motife is responsible for the <two>Ca²⁺-binding</two>, though? A <one>helix-loop-helix</one> (<two>HLH</two>) motife.
+- How do we call <one>folding possibilities</one> of proteins? The <one>conformation space</one>.
+- Aus Sicht der Strukturbiologie: wieso wirkt <one>Quecksilber</one> toxisch? Quecksilber kann Enzyme und Proteine destabilisieren, indem es an deren Sulfhydryl-Gruppen bindet.
+- Bei der <two>Bildung einer Peptidbindung zwischen Aminosäuren</two> geht <one>Wasser</one> (H₂0) verloren. Gibt es einen einfachen Weg, wie wir uns merken können, wer diese drei Atome liefert? Ja - und zwar sind die Enden der Aminosäuren innerhalb der Zelle geladen; wir haben also eine <one>-COO (minus)-Gruppe</one> sowie eine <one>-NH3 (⁺)-Gruppe</one>. Daraus folgt das die -COO Gruppe nur ein O liefern kann; und die -NH3 Gruppe nur zwei H-Atome liefern kann.
+- What is <one>the major unsolved problem</one> in <two>structural molecular biology</two>? How to <one>predict the three-dimensional structure of a protein</one>.
+- How are <one>regions of a protein</one> called that do not form a secondary structure? A <one>random coil</one>.
+- Every protein has <one>a free amino terminus</one> at one end and <one>a free carboxy terminus</one> at the other end, except for ... ? A few <one>cyclic polypeptides</one>.
+- Proteins are not static structures. They are best represented by ... ? An ensemble of possible conformations.
+- In general: <two>where</two> in a large protein can we find <one>Alpha-helices</one>? Along the <one>outside surface of a protein</one>.
+- In general, <one>where</one> do <two>Beta-Hairpin turns</two> occur? They occur between <one>two antiparallel beta-strands</one>.
+- A <one>chaperone</one> generally binds to ..? A <one>partly folded polypeptide chain</one>.
+- In der Strukturbiologie: wofür steht die Abkürzung <one>SCOP</one>? <one>Structural classification of proteins</one>. URL: https://en.wikipedia.org/wiki/Structural_Classification_of_Proteins_database
+- <one>PDB</one> contains a lot of proteins. How many in the year <two>2016</two>? About <one>67.700</one>.
+- Warum sind nicht alle Werte im Ramachandran-Diagramm möglich zwischen phi und psi Bindungswinkeln? Weil es zu <one>Kollisionen zwischen den Atomen</one> kommen kann; dies ist energetisch gesehen ungünstig.
+- A <one>fusion tag</one> may act as ... ? as <one>a nucleation site for the folding of the target protein</one>.
+- Name a <one>major advantage of NMR-spectroscopy</one> compared to <two>X-ray crystallography</two>. A: We can <one>study protein structures in solution</one>.
+- <two>Wie</two> bestimmt man den <one>isoelektrischen Punkt</one> von Proteinen experimentell? Mit Hilfe einer <one>Titrationskurve</one>. URL: https://de.wikipedia.org/wiki/S%C3%A4ure-Base-Titration#Verlauf_von_Titrationskurven
+- Does <one>proline</one> contribute to overall folding? Yes, <one>by forming bends</one>.
+- Was kann die <one>EF-Hand</one> binden? <one>Ca²⁺</one>. URL: https://en.wikipedia.org/wiki/EF_hand
+- For <one>X-ray</one>, the crystal is mounted between ... ? Between an <one>X-ray source</one> and an <one>X-ray detector</one>.
+- The <one>folding process</one> goes from a high energy unfolded state to a low energy native state, through ... states. A: <one>metastable intermediate states</one>.
+- Strictly speaking, from the point of structural biology, the term <one>hydrophobic proteins</one> is misleading. Why? Because it is <one>the water</one> which dislikes the dissolved non-polar groups.
+- Nenne drei <one>Kenngrößen der Alpha-Helix</one>. A: (1) <one>Ganghöhe</one> (2) <one>Anstieg</one> (3) <one>Drehung</one>
+- <one>Starke Helix-Brecher</one> sind zum Beispiel <two>Glycin</two> oder <two>Prolin</two>. Es gibt jedoch auch zwei schwache Helix-Brecher, ebenso Aminosäuren. Welche zwei sind dies? (1) <one>Asparagin</one> (2) <one>Tyrosin</one>
+- The <one>PDB</one> (Protein Data Bank) contained how many proteins in <two>2005</two>? Roughly <one>25.000 proteins</one>, determined by X-ray crystallography.
+- Historisch betrachtet: <two>welche Proteine</two> konnten zuerst <one>entdeckt</one> werden? Jene die <one>reichlich</one>, und dadurch einfach zu isolieren, <one>vorhanden waren</one>.
+- The <two>intrinsic factors</two> that influence <one>protein solubility</one> are defined primarily by ... ? By the amino acids on the protein surface.
+- In <one>structural biology</one>: what is meant with the term <two>docking</two>? This refers to <one>the interaction between proteins</one>.
+- Proteine können auf <two>Ligandenbindung</two> mit einer <one>Konformationsänderung</one> reagieren. Gib hierzu ein Protein-Beispiel an. A: <one>Calmodulin</one>.
+- For <one>a general classification scheme</one>: which <two>three types of proteins exist</two>? (1) <one>structural proteins</one> (2) <one>membrane proteins</one> (3) <one>globular proteins</one>
+- Warum ist <one>die Konformationsänderung von Lactoferrin</one> wichtig? Weil andere Proteine diese Änderung erkennen können.
+- The <one>secondary structure</one> of a protein depends solely on ...? <one>Hydrogen bonding</one>.
+- Erreichbare Auflösung bei der <one>Einzelkristallröntgenbeugung</one>? <one>1 Angstrom</one>.
+- In der Strukturbiologie: was meinen wir mit <one>MAD</one>? <one>Multi-wavelength anomalous diffusion</one>.
+- <one>Protein space</one> lies within ... ? <one>Chemical space</one>. URL: https://en.wikipedia.org/wiki/Chemical_space
+- <two>Christian Anfinsen</two> worked with <one>which enzyme</one> in particular, in order to demonstrate that proteins can refold? The enzyme <one>ribonuclease</one>.
+- Wieso ist <one>die globuläre Kugelform bei Proteinen</one> so häufig zu sehen? Dies ist <one>eine Konsequenz des hydrophoben Effekts</one>.
+- Was ist bei der Verwendung eines <one>Protease-Inhibitor Cocktails</one> zu beachten? <two>Zellen enthalten verschiedene Proteasen, die Proteine unspezifisch degradieren mögen</two>. Organellen können zerstört werden und so auch ihre spezifischen Proteasen freisetzen. Man sollte <one>nur soviel Inhibitoren hinzufügen, um die Proteolyse, die man verhindern möchte, aufzuhalten</one>.
+- Which <one>direction</one> (left-handed versus right-handed) is <two>FORBIDDEN</two> for an alpha-helix formed by L-amino acids? A <one>left-handed alpha-helix</one> is not allowed for the <two>L-amino acids</two>.
+- Nenne zwei Strukturmotive, die <one>beta</one> in ihrem Namen inkludieren. A: (1) <one>beta-Sandwich</one> (2) <one>beta-Barrel</one>
+- The <one>alpha helix</one> is also known as the <two>3.613-helix</two>. What does the 13 indicate here? <one>13 atoms</one> are involved in the ring formed by the hydrogen bond.
+- <one>Fhkl</one> is a mathematical function, used in x-ray crystallography that describes the amplitude and phase of a wave diffracted from crystal lattice planes, characterized by ... indices h,k,l. A: <one>Miller indices</one>.
+- What are <one>molten globules</one>? <two>Molten globules</two> are compact, <one>partially folded conformations</one> of proteins that have near-native compactness.
+- How does <one>comparative modeling</one> work? <one>Comparative modeling</one> uses an existing 3D structure of a protein to model the geometry of a structurally unknown target with similar amino acid sequence.
+- Do <one>cis-peptide bonds</one> exist in nature? Yes, in <two>cyclic dipeptides</two> for example, as can be found in the <two>diketopiperazines</two>. URL: https://en.wikipedia.org/wiki/Diketopiperazine
+- In structural biology: what is meant with the <one>hydrophobic effect</one>? These are mostly the hydrophobic sidechains in the interior of a protein (or a protein structure).
+- Why is the <one>N-terminal part</one> of the <three>lactate dehydrogenase</three> important? Because it will interact with other subunits, thus keeping the whole complex together.
+- Einfaches Merkschema (Mnemonic) für das <one>Greek key motife</one>? <one>rauf-runter-rauf-runter</one>.
+- Es gibt das <one>CATH protein structure classification</one>. Wofür steht die Abkürzung <two>CATH</two>? (1) <one>Class</one> (2) <one>Architecture</one> (3) <one>Topology</one> (4) <one>Homology</one>
+- One strategy used to design a stronger, better alpha-helix is via <one>capping</one>, in particular ... ? <one>N-capping via Asparagin</one>.
+- Hat <one>Zink</one> einen <two>Einfluss auf den pKA von Aminosäuren</two>? Ja. <royalblue>Zink</royalblue> bindet die Aminosäuren Histidin und Cystein und <one>senkt dadurch deren pKa</one>.
+- Nenne zwei <one>3D-Eigenschaften</one> der Peptidbindung. A: (1) Planarität (2) <one>Konformation</one>
+- Eine <one>Peptidbindung</one> ist eine ... Bindung zwischen der Carboxygruppe einer Aminosäure und der Aminogruppe des α-Kohlenstoffatoms einer zweiten Aminosäure. A: Eine <one>amidartige Bindung</one>.
+- Name a program for <one>Peptide helicity prediction</one>. A: <one>AGADIR</one>.
+- Allgemein gilt bei <one>Glycin</one> was in einem Protein? Glycin findet sich oft an Positionen in der Peptidkette, die sich bewegen oder eine Art <one>Gelenk des Proteins</one> darstellen.
+- What is meant with the term <one>hydrophobicity profile</one>? This is when we use a hydrophobicity scale that assigns a value to each amino acid, and to then plot the variation of hydrophobicity along the sequence of the protein.
+- <one>Carbon-carbon bond distance</one>, in Angstrom? <one>1.5 Angstrom</one>.
+- <one>Domain swapping</one> is a structural phenomenon that plays an important role in the mechanism of ... of some proteins. A: <one>Oligomerization of some proteins</one>.
+- The <one>electrostatic interactions</one> can function within a range of about ... ? <one>15 Angstrom</one>.
+- In der Strukturbiologie: was meinen wir mit einem <one>positiven allosterischen Effekt</one> und mit einem <one>negativen allosterischen Effekt</one>? (1) <one>Positiver allosterischer Effekt</one>: dies ist dann der Fall, wenn die Bindung eines Liganden die Bindung eines <mediumseagreen>anderen</mediumseagreen> Liganden erleichtert. (2) <one>Negativer allosterischer Effekt</one>: dies ist dann der Fall, wenn die Bindung eines Liganden die Bindung eines <mediumseagreen>anderen</mediumseagreen> Liganden erschwert.
+- Nenne ein Beispiel für Proteine, die <one>amphiphile Bereiche</one> besitzen. A: Die <one>Apolipoproteine</one>.
+- What is the biggest problem in <one>X-ray crystallography</one> itself, aside from the difficulty of creating a pure protein crystal? An <one>inability to measure phases directly</one>.
+- The <one>molten globule</one> should not be viewed as a single structural entity but instead as ...? An <one>ensemble of related structures that are rapidly interconverting</one>.
+- Ordne die 20 Aminosäuren nach ihrer <one>Hydrophobizität</one>, beginnend mit der hydrophobsten Aminosäure. A: <one>IVL-FCM-AGT-SWY-PHE-QDN-KR</one>.
+- Was heisst es wenn wir sagen das ein Protein <one>atmet</one>? Das ein Protein nicht starr ist, sondern <one>konformationellen Fluktuationen unterliegt</one>.
+- Say something about the <one>concentration</one> of hemoglobin in <lightseagreen>red blood cells</lightseagreen>. A: It is <one>almost as high as in the crystalline state</one>.
+- What is <one>apomyoglobin</one>? This is myoglobin without the <one>heme prosthetic group</one>. URL: https://en.wiktionary.org/wiki/apomyoglobin
+- In regards to structural biology: what did <one>Levinthal</one> point out? That proteins cannot fold by random search in <one>conformation space</one>.
+- In X-ray protein research: what is meant with the term <one>model building</one>? This is the process where the electron density map is <one>interpreted in terms of a set of atomic coordinates</one>.
+- What happens if we add an increasing amount of <one>Guanidinium chloride</one> to proteins in solution? These <one>proteins will unfold</one>. URL: https://en.wikipedia.org/wiki/Guanidinium_chloride
+- Is <one>water</one> part of a molecule, as far as structural biology is concerned? This depends; internally bound water molecules can be regarded as <one>integral parts of the protein structure</one> at hand.
+- Warum liefern <one>Röntgenstrahlen</one> die bestmögliche Auflösung? Da die Wellenlänge der Röntgenstrahlen ungefähr der einer <one>kovalenten Bindung</one> entspricht.
+- Was bedeuten <one>weiße Flächen</one> im Ramachandran-Diagramm? Dies sind Bereiche, die infolge starker sterischer Wechselwirkungen <one>unzulässige Torsionswirkel</one> aufweisen.
+- The <one>strength of a hydrophobic interaction</one> is proportional to ... ? The surface area that is hidden from water.
+- Nenne einen <one>häufigen Reflex</one> von Proteinen. A: Die Bindung eines Liganden induziert im Protein eine <one>Konformationsänderung</one>.
+- What are <one>Thermosomes</one>? Thermosomes, found in some <one>Archaea</one>, are hollow balls inside which proteins are folded. URL: https://en.wikipedia.org/wiki/Thermosome
+- What is the main implication derived from the existence of the <one>Levinthal Paradox</one>? That proteins have evolved <one>mechanisms of efficient folding</one>.
+- How many <one>protein families</one> were known in the year 2013? At the least <one>14.830</one>.
+- Was ist das <one>Friedel law</one>? Eine Eigenschaft von Fourier Transformationen von reellen Funktionen.
+- The basic repeating unit of a polypetide chain is ... ? <one>NH-Calpha-H-CO</one>.

data/lib/studium/exam_topics/system_biology_and_synthetic_biology

@@ -0,0 +1,101 @@
+# =========================================================================== #
+# === System Biology and Synthetic Biology
+#
+# Everything about system biology and synthetic biology.
+#
+# This presently also includes parts about protein engineering, but
+# this may be moved into another topic one day - something like
+# "protein_engineering_and_enzyme_engineering" or something
+# like that.
+# =========================================================================== #
+
+- The term <one>'synthetic biology'</one> is a surprisingly old term, originated in the year ... by <two>Stéphane Leduc</two>. A: In the year <b>1912</b>.
+- The main engineering material of living cells is ... ? <one>Protein</one>.
+- The idea of <one>Biobricks</one> in synthetic biology dates back at the least to which year? <one>2003</one>.
+- In synthetic biology: <one>IGEM</one> stands short for ... ? <one>International genetically engineered machines</one>.
+- What is meant with the term <one>minimal genome</one>? This refers to <one>the smallest genome that is sufficient to create, maintain, and replicate itself</one>.
+- The <one>'bactoblood'</one> E. coli could produce ... which substance? <one>Hemoglobin</one>.
+- One of the best <one>biological batteries</one>, in general, is ... ? The <one>microbial fuel cell</one>.
+- In <one>secondary structure propensity</one>, we tend to normalize towards which aminoacid typically? Towards <one>Alanine</one>. []
+- <one>Experimental protein engineering</one> may occur through <two>irrational design</two>. Give another word for irrational design. A: <one>In-vitro evolution</one>.
+- <one>Process algebra</one> can be used to model ... what kind of systems? <one>Concurrent systems</one>.
+- Name <one>four different operations</one> that we can apply to two different sets. A: (1) "equality" (2) "union" (3) "intersection" (4) <one>difference</one>
+- The <one>ChIP-on-chip technique</one> combines which two other techniques? (1) <one>chromatin immunoprecipitation</one> (<two>ChIP</two>) (2) DNA microarray technology ("chip")
+- What does the <one>system-level approach</one> attempt to do? It attempts to <one>consider all the components of a system</one>.
+- In a <one>Gillespie model</one>: if we draw a flux-system, what do thicker flux-arrows indicate? These flux-states are more likely to happen than the not so thick flux-states.
+- <one>Chimeric antibodies</one> typically <two>combine domains from which two species</two>? (1) <one>Mouse</one> (2) <one>Human</one> []
+- In synthetic biology: what is meant with the abbreviation <one>UAA</one>? <one>Unnatural amino acid</one>.
+- The "Biomass objective function" (BOF) for organisms is similar in spirit to ... ? The <one>sum formula of organic molecules</one>.
+- <one>Which functions</one> could be used as a general model of gene expression, in system biology? <one>Hill-type functions</one>.
+- What is <one>Photopharmacology</one>? <one>Photopharmacology</one> uses photoswitchable drugs that can be reversibly activated with light for interaction with their target receptors or enzymes.
+- A <one>genetic repressilator</one> typically includes <two>n different genes</two>? <one>Three</one>.
+- Provide another name for <one>metabolic pathways</one>, the system-biology view. A: <one>Reaction networks</one>.
+- In <one>mRNA display</one>: can <two>non-natural amino acids</two> be used? Yes. []
+- <one>RBM</one> (rule-based models) consist of a set of rules, naturally, and a set of ... ? <one>Objects</one>.
+- <one>Multifunctional immunoglobulins</one> created in the lab typically have which two general features? (1) <one>Antigen binding</one> (2) various <one>effector functions</one>
+- Name a huge problem in <one>predictions</one> established through systems biology only. A: Even if a prediction may seem to hold true under several conditions, it may fail with the next. This means that there is a "large degree of uncertainty".
+- Name two ways how to <one>computationally determine the interactome</one>. A: (1) "Genomic context" (2) <one>Co-Evolutionary</one>
+- Give another name for a <one>cell</one>, from the point of view of <three>synthetic biology</three>. A: A <one>chassis</one>. []
+- <one>Process algebra</one> is also called ... ? Labeled transition systems.
+- In <one>computational enzyme engineering</one>: can <two>mutations</two> be used in order to stabilize the transition state? Yes. []
+- In <one>enzyme engineering</one>: <two>why</two> do we wish to create enzymes that function in organic solvent? Because <one>some substrates are not solvent in water</one>, so we lack enzymes that can process such substrates.
+- When an <one>orthogonal ribosome</one> is constructed, what is meant with that term actually? That we will mutate (thus engineer) the Shine‐Dalgarno sequence as well as the anti‐Shine‐Dalgarno sequence. That way we obtain mRNAs and ribosomes which are unable to interact with endogenous mRNAs and ribosomes in the given cell.
+- Can we reconstruct the hypergraph from the <one>stoichiometric matrix</one>? No; information was already lost during that conversion.
+- In <one>Ribosome evolution</one> we seek to engineer what here? We seek to engineer the interaction between the ribosome and the messenger RNA.
+- A fusion protein contains how many domains minimum? Two. 
+- <one>Ribosome evolution</one> attempts to engineer which interaction? The <one>interaction between the ribosome and the messenger RNA</one>.
+- Name a key approach in <one>synthetic biology</one>. A: <one>Systematic design</one>.
+- Name three goals that may occur through <one>protein engineering</one>. A: (1) a <one>change in substrate specificity</one> (2) <one>increased stability to the temperature</one> (3) <one>extremes of pH</one>
+- In system biology: the abbreviation <one>FBA</one> stands for ... ? <one>Flux balance analysis</one>.
+- Name two very important objective functions in flux balance analysis. A: (1) Maximum biomass yield (2) Maximum product yield
+- In der <one>synthetischen Biologie</one>: die <two>second generation oscillators</two> erlaubten es die Frequenz einzustellen, über ... ? Die <one>IPTG Konzentration</one>.
+- The <one>TET-ON expression system</one> makes use of the TRA. TRE stands for ... ? <one>Tetracycline response element</one>.
+- One optimization that is often made in <one>protein engineering</one>   is to increase the stability of proteins at higher temperature. Contrast the average Tm (melting temperature) between proteins used in biology, and those used in biotech. A: (1) Proteins used in biology have a Tm of about 40°C. (2) Proteins used in biotechnology tend to have a Tm of about 80°C - at the least in <royalblue>washing powder</royalblue>.
+- For protein engineering we can also make use of which PCR, in order to add multiple mutations into the protein? We can make use of <one>mega-primer snythesis</one>.
+- Can we make use of PTMs in a <one>Yeast Surface Display</one>? Yes.
+- Give a better name for <one>Yeast Display</one>. A: <one>Yeast Surface Display</one>.
+- In <one>protein engineering</one>: what do we mean with genotype-connected-to-the-phenotype? For example when a protein is connected to the DNA that codes for it; in this case we can say that the genotype is connected to the phenotype.
+- Are <one>quantum mechanics</one> employd in <two>enzyme design</two>? Yes.
+- In irrational evolution of proteins and enzymes: the design is based on ... principles? On <one>thermodynamic principles</one>.
+- In irrational evolution of proteins and enzymes (protein design), we typically start with ... ? A gene sequence, which is then mutated (<royalblue>mutagenesis</royalblue>).
+- Name two different strategies for <one>designing a novel enzyme</one>. A: (1) <one>rational protein design</one> (2) <one>irrational in-vitro evolution</one>
+- In computational design of proteins, the backbone can be changed via ... ? <one>Mutations</one>.
+- In <one>computational design of proteins</one>: is the main backbone of a protein modelled computationally? Only very rarely.
+- In computational design of proteins, there is a trade-off in regards to accuracy and speed. How could we improve the speed of our calculations, for designing the catalytic core of an enzyme or the base area of a protein? we could simply <one>use fewer amino acids</one>, if possible.
+- In <one>computational engineering</one> of proteins, how can we compute the transition state? We <one>use quantum mechanics</one>.
+- In <one>computational enzyme engineering</one> we may wish to design a hole in an enzyme, in order to put the substrate into that hole. Name an aminoacid that we could wish to use here. A: Alanine, because it is a very small aminoacid.
+- In <one>enzyme engineering</one>: name a way how the P450 enzyme could be improved, for engineering purposes. A: We could design a P450 enzyme that does not require additional proteins or co-factors.
+- Why does the <one>DNA shuffling procedure</one> have this name peculiar name? Because we cut genes together, aka use different pieces from different organisms, before doing the <one>reassembly PCR</one>.
+- In the DNA shuffling procedure for engineering proteins or enzymes, how much sequence identity should be on the gene level, at the least? At the least about 70%.
+- In <one>protein engineering</one>: in designing protein-protein interactions, when it comes to the interface of the protein ... what would be a useful advice here? We should pick the variant that gives us <one>the lowest (overall) energy</one>.
+- Name two reasons why we may use computational methods for protein design, as well as directed evolution for protein design. A: (1) we could try to create novel drugs (2) we could try to understand protein evolution (in living beings as well)
+- In <one>protein engineering</one>: what is meant with <two>binding specificity</two>? This refers to how well a given protein may bind to the desired target, versus other targets.
+- When designing <one>protein-protein interactions</one>, , what computational method is useful here for determining where proteins may interact? We may employ <one>computational saturated mutagenesis</one>.
+- What is the holy grail in <one>protein engineering</one>, if we have more than one protein as our targets? To <one>optimize the energy function for protein-protein interactions</one>.
+- In <one>protein engineering</one> we can distinguish between <two>positive design</two> and <two>negative design</two>. What is meant with these terms? (1) <royalblue>positive design</royalblue>: this refers to design of the protein against the <one>desired target</one> (2) <royalblue>negative design</royalblue>: this refers to design of the protein against an  <one>undesired target</one>
+- Can <one>enzymes</one> be <two>computationally designed</two>? Yes.
+- The <one>DNA shuffling procedure</one> can be used to create novel proteins/enzymes. In which year was this technique develope? In <one>1994</one>.
+- We can design enzymes (enzyme engineering). Name two goals that we may have here, for enzymes. A: (1) achieve better stability of these enzymes (2) achieve higher activity of these enzymes
+- Name three different methods for creating protein diversity or enzyme diversity. A: (1) saturated mutagenesis-probe (2) error-prone PCR (which can add 1-2 mutation per gene) (3) DNA-shuffling in order to recombine DNA sequences from different proteins
+- The word <one>digraph</one> is an abbreviation to ... ? <one>Directed graph</one>.
+- "Linear programming" was also used in world war, such as by solving what kind of problems? Ensuring a <one>healthy supply chain</one>.
+- What is meant with the term <one>panomics</one>? This refers to the range of molecular biology technologies, including genomics, proteomics, metabolomics, transcriptomics, and so forth, in particular when these omics are integrated into a combined use.
+- Organisms adapt to environmental ... ? <one>Variations</one>.
+- Foldamers are ... ? Non-standard polymer building blocks.
+- In chemistry, SIR models are often used for ...-systems. A: "combustion-systems."
+- The "SIR model" is useful for modeling "diseases". What does SIR stand for? (1) S ... susceptible state (2) I ... infected state (3) R ... recovered state
+- In stochastic simulation, in system biology, which algorithm is the best one? The Gillespie-algorithm.
+- A popular algorithm to solve LP (linear programming) is called ... ? "Simplex method".
+- Name a qualitative difference between graphs and hypergraphs that is also useful for system biology. A: (1) "Graphs":      can express "one-to-one"   vertex relations (2) "Hypergraphs": can express "many-to-many" vertex relations
+- System Biology has to deal with "biological data". This data often poses which two major problems? (1) often only qualitative or semi-quantitative, rather than quantiative (2) problems such as "noise", "measurement errors" or "missing data points"
+- What does the "clustering coefficient" measure in networks? It measures how strong the neighborhood of a vertex deviates from a clique.
+- The "Interactom" is ... ? The list of "all protein-protein interactions".
+- Name an objective of systems biology. A: The "understanding of network behavior".
+- Systems Biology is based upon ... data. A: "omics" data.
+- A graph is a tupel of which two sets? (1) the "vertex set" (2) the "edge set"
+- Do "Metabolic networks" hold enough information for a direct reconstruction of the "phylogenetic relationships"? Yes.
+- ChIP-on-chip allows to study binding sites of DNA-binding proteins on a ... basis. A: "genome-scale basis".
+- Metabolic networks are "scale-free"? No; they are "scale-rich networks".
+- Name an important reason as to why we may have to employ system biology, as opposed to solely using other methods from biology. A: No single methodology alone is able to cover everything.
+- Name an important goal related to (molecular) biology that system biology aims to tackle. A: Figure out how a cell works.
+- Systems biology studies biological systems by systematically ... ? "perturbing them", aka biologically, genetically or chemically.