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data/lib/studium/exam_topics/system_biology_and_synthetic_biology

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+# =========================================================================== #
+# === 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.
+# =========================================================================== #
+
+- Synthetic biology promises to automate ... ? <one>evolution</one>.
+- Name <one>three goals</one> that may be achieved via <two>protein engineering</two>. 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: what is meant with the term <one>phenotypic plasticity</one>? This refers to the fact that <one>the same genotype may yield different phenotypes</one>.
+- Can we <one>reconstruct the hypergraph</one> <two>from the</two> <three>stoichiometric matrix</three>? No; information was already lost during that conversion.
+- The <one>'bactoblood'</one> <two>E. coli</two> <three>could produce ... which substance</three>? <one>Hemoglobin</one>.
+- In <one>secondary structure propensity</one>, we <two>tend to normalize towards which aminoacid typically</two>? Towards <one>alanine</one>.
+- In <one>computational design of proteins</one>: <two>is the main backbone of a protein modelled computationally</two>? Only <one>very rarely</one>.
+- Give <one>an example of an intensively measured multi-cellular organism</one>. A: <one>C. elegans</one>.
+- In <one>protein engineering</one> we can distinguish between <two>positive design</two> and <two>negative design</two>. <three>What is meant with these terms</three>? (1) <one>positive design</one>: this refers to design of the protein against the <two>desired target</two> (2) <one>negative design</one>: this refers to design of the protein against an  <two>undesired target</two>
+- In <one>ribosome evolution</one> we seek to engineer what here? We seek to <one>engineer the interaction between the ribosome and the messenger RNA</one>.
+- Name <one>three different methods</one> for creating protein diversity or enzyme diversity. A: (1) <one>saturated mutagenesis-probe</one> (2) error-prone PCR (which can add 1-2 mutation per gene) (3) DNA-shuffling in order to recombine DNA sequences from different proteins
+- In <one>computational engineering</one> of proteins: <two>how can we compute the transition state</two>? We <one>use quantum mechanics</one>.
+- Name <one>an important goal</one> related to (molecular) biology that system biology aims to tackle. A: Figure out how a cell works.
+- Combine the two expressions <one>system biology</one> and <two>reverse engineering</two> into a meaningful statement. A: System biology can be used to reverse engineer metabolic networks from experimental data.
+- The First International Conference on Systems Biology, ICSB2000, was held in which city? <one>Tokyo</one>.
+- A model behaviour, originating from reallife, can turn out to be physically impossible. What may be required here? We may have to do a reality-check, to see whether a model can be true/realistic.
+- The <one>father of biological cybernetics</one> is ... ? <one>Norbert Wiener</one>.
+- Die <one>Hachimoji-DNA</one> in der synthetischen Biologie: wofür steht hachimoji? Für <one>acht Buchstaben</one> (Hoshika et al. 2019).
+- Name <one>three different safeguard strategies</one> that may be used in synthetic biology, for creating new, synthetic organisms. A: (1) Engineered Auxotrophy (2) Induced Lethality (3) Gene Flow Prevention
+- Name one of the most important principle found in <one>synthetic biology</one>. A: <one>Modularity</one>.
+- What is meant with the term <one>panomics</one>? This refers to <one>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</one>.
+- <one>RBM</one> (<two>rule-based models</two>) consist of a set of rules, naturally, and a set of ... ? <one>Objects</one>.
+- Name an objective of systems biology. A: To <one>understanding of network behavior</one>.
+- In <one>irrational evolution of proteins and enzymes</one>: the design is based on ... principles? On <one>thermodynamic principles</one>.
+- Name <one>two ways</one> how to <two>computationally determine the interactome</two>. A: (1) <one>Genomic context</one> (2) <one>Co-Evolutionary</one>
+- 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>.
+- 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: <one>Alanine</one>, because it is a very small aminoacid.
+- <one>Process algebra</one> is also called ... ? <one>Labeled transition systems</one>.
+- Are <one>quantum mechanics</one> employd in <two>enzyme design</two>? Yes.
+- 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>.
+- One of the best <one>biological batteries</one>, in general, is ... ? The <one>microbial fuel cell</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>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".
+- Give another name for a <one>cell</one>, from the point of view of <three>synthetic biology</three>. A: A <one>chassis</one>.
+- 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.
+- <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>.
+- 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>.
+- 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>.
+- 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.
+- 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 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>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.
+- 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>.
+- 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
+- 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>.
+- 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".
+- 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.
+- Systems biology studies biological systems by systematically ... ? "perturbing them", aka biologically, genetically or chemically.