General course knowledge
This concept describes the passage of information from DNA to RNA to protein
What is the Central Dogma of Molecular Biology?
This metabolic reconstruction represents metabolites in rows and reactions in columns. It is a numerical description which reactions consume/produce which metabolites
What is the stoichiometric matrix?
(A phylogenomic study of the MutS family of proteins) For the phylogenomic trees in this paper, proteins with fewer branches separating them were more similar in this regard
What is sequence alignment (or protein function)?
(Cluster analysis and display of genome-wide expression patterns) While previous works studied gene-expression purely numerically, this paper introduced analysis of large-scale expression data by this visual comparison?
What is color?
CBE 246 is held in this lecture hall
What is Kaufman hall?
While classical molecular biology often uses a reductionist approach (i.e. measuring the regulation of one gene), systems biology requires this approach, which looks at large scale interactions in the entire system
What is a holistic approach?
According to the summation theorem of metabolic control analysis, the sum of all control coefficients must equal this number
What is 1?
(Noise in Gene Expression Determines Cell Fate in Bacillus subtilis) Here, the authors measured two fluorescent probes to determine if ComK expression was caused by which these two types of noise (name both)
What is intrinsic and extrinsic noise?
(Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles) In GSEA, expression data is ranked according to this
This is the full name of CBE246
What is "Systems Biology: Intracellular Network Identification and Analysis"?
What is regulation?
To obtain a set of fluxes using flux balance analysis (FBA), you need a metabolic model, constraints to your solution space, and this entity
What is an objective function?
(Protein Sectors: Evolutionary Units of Three-Dimensional Structure) This paper derived its initial statistical noise separation techniques from this non-life-sciences discipline?
What is economics (or finance, stock-market, etc.)?
(Noise in Gene Expression Determines Cell Fate in Bacillus subtilis) To lower the average ComK protein levels in the cell, the authors modified this component of the ComK gene to reduce its translational efficiency
What is the start codon?
This is the record number of extra chairs Richard has brought into class
What is 3?
When assuming a quasi or pseudo steady-state, these entities are equivalent to rates in a linear set of reactions
What are fluxes?
While control coefficients and elasticities help define how intracellular factors influence flux, these values help describe how fluxes react to other factors
What are response coefficients?
(Systems-level analysis of mechanisms regulating yeast metabolic flux) To generate 25 different metabolic conditions, the authors grew yeast in chemostats that, by changing the dilution rate, allowed them to set this value
What is the growth rate?
(Using mathematical models to help understand biological pattern formation) This paper modeled how these two factors impact the concentration of a chemical at a given time and place (name both)
What is diffusion and reaction?
This is the temperature that the room's thermostat is set to
What is 76ºF?
For a given enzyme-catalyzed reaction S-->P, this concept describes: Keq = (kcat+/KM,S) / (kcat-/KM,P)
What is the Haldane relation?
For a metabolic system at steady-state, there can be this many solutions to the flux balance equation (name all three)
What is 0, 1, and infinity?
(Maximum entropy models for antibody diversity) The authors plotted distribution probability against rank to visually consider whether or not the D region sequences followed this law
(Protein Sectors: Evolutionary Units of Three-Dimensional Structure) This paper discovered three protein sectors that were related to these biochemical characteristics of the serine proteases (name at least two of three)
What is substrate specificity (red), thermal stability (blue), and catalytic activity (green)?
This man wrote the textbook on Metabolic Control Analysis
Who is David Fell?