Level 2 — RecallSystems Biology & Frontiers

Systems Biology & Frontiers

⏱ 30 minutes40 marksprintable — key stays hidden on paper

Chapter 6.5 — Systems Biology & Frontiers

Level: 2 — Recall (definitions, standard textbook problems, short derivations) Time Limit: 30 minutes Total Marks: 40

Q1. Define systems biology and state what is meant by a holistic (as opposed to reductionist) approach to studying an organism. (4 marks)

Q2. A gene regulatory network (GRN) can be represented as a directed graph. (a) State what the nodes and edges represent in a GRN. (2 marks) (b) Distinguish between an activating and a repressing regulatory interaction. (2 marks)

Q3. Explain what a metabolic network model represents. In your answer, define a flux and briefly state the principle behind Flux Balance Analysis (FBA). (5 marks)

Q4. Describe a signal transduction network. Name the three general stages of signal transduction (reception, transduction, response) and give one example of a second messenger. (4 marks)

Q5. Define multi-omics integration. List four distinct "omics" layers and state what each measures. (5 marks)

Q6. Define emergent behavior in a biological system and give one concrete biological example. (3 marks)

Q7. Consider a simple mathematical model of gene expression where mRNA is produced at a constant rate $k$ and degraded at a rate proportional to its concentration with constant $\gamma$ : $\frac{dM}{dt} = k - \gamma M$ (a) Derive the steady-state concentration $M_{ss}$ . (2 marks) (b) If $k = 20\ \text{molecules min}^{-1}$ and $\gamma = 0.5\ \text{min}^{-1}$ , calculate $M_{ss}$ . (2 marks)

Q8. Define the human microbiome and describe two systemic effects it can have on host health. (4 marks)

Q9. (a) Explain what single-cell sequencing measures and give one advantage over bulk sequencing. (2 marks) (b) Define spatial transcriptomics in one sentence. (1 mark)

Q10. (a) Explain what a minimal cell / synthetic genome project (e.g. JCVI-syn3.0) aims to determine. (2 marks) (b) State two ethical or societal challenges raised by modern frontier biology. (2 marks)

End of paper

Answer keyMark scheme & solutions

Q1. (4 marks)

Systems biology = the study of biological systems as integrated wholes, focusing on the interactions between components (genes, proteins, metabolites) rather than the components in isolation. (2)
Holistic approach: examines the system's collective/network-level behavior so that properties emerging from interactions can be understood; contrasted with reductionism which studies each part separately. (2) Why: Definition tests recall of the discipline's core premise (whole > sum of parts).

Q2. (4 marks) (a) Nodes = genes (or their products/transcription factors); edges = regulatory interactions/influences of one gene on another. (2) (b) Activating interaction increases target gene expression; repressing interaction decreases it. (2)

Q3. (5 marks)

Metabolic network model = representation of all biochemical reactions (and the metabolites they interconvert) in a cell, linking substrates and products via enzymes. (2)
Flux = the rate at which material flows through a given reaction (e.g. mmol gDW⁻¹ h⁻¹). (1)
FBA principle: assumes steady state (production = consumption for each internal metabolite), applies stoichiometric mass-balance constraints, and optimizes an objective (e.g. biomass/growth) using linear programming. (2)

Q4. (4 marks)

Signal transduction network = the connected pathways by which cells detect extracellular signals and convert them into intracellular responses. (1)
Three stages: reception (ligand binds receptor), transduction (relay/cascade, often phosphorylation), response (change in cell activity/gene expression). (2)
Example second messenger: cAMP (or Ca²⁺, IP₃, DAG). (1)

Q5. (5 marks)

Multi-omics integration = combining data from multiple molecular layers to build a comprehensive systems-level view. (1)
Any four (1 each): Genomics (DNA sequence/variants); Transcriptomics (RNA/gene expression); Proteomics (proteins/abundance); Metabolomics (metabolites/small molecules); Epigenomics (DNA methylation/chromatin marks). (4)

Q6. (3 marks)

Emergent behavior = a system-level property that arises from interactions among components and is not present in / predictable from any single component alone. (2)
Example: circadian rhythms, network oscillations, quorum sensing, cell differentiation patterns, or consciousness. (1)

Q7. (4 marks) (a) At steady state $\frac{dM}{dt}=0 \Rightarrow k-\gamma M_{ss}=0 \Rightarrow M_{ss}=k/\gamma$ . (2) (b) $M_{ss}=20/0.5 = 40$ molecules. (2)

Q8. (4 marks)

Microbiome = the collective community of microorganisms (bacteria, archaea, fungi, viruses) and their genes inhabiting the human body. (2)
Two systemic effects (1 each): aids digestion/vitamin synthesis; trains/modulates the immune system; influences metabolism/obesity; gut–brain axis effects on mood/behavior; protection against pathogens. (2)

Q9. (3 marks) (a) Single-cell sequencing measures the genome/transcriptome of individual cells, revealing cell-to-cell heterogeneity hidden by bulk averaging. (2) (b) Spatial transcriptomics = measuring gene expression while preserving the spatial (positional) location of cells within a tissue. (1)

Q10. (4 marks) (a) Minimal cell/synthetic genome projects aim to determine the smallest set of genes necessary and sufficient for life, by building/reducing a genome and testing viability. (2) (b) Two of: biosafety/biosecurity risks, dual-use concerns, ownership/patenting of life, data privacy (genomic), gene-editing ethics, equity of access. (2)

[
  {"claim":"Steady state Mss = k/gamma general formula", "code":"k,g,M=symbols('k g M',positive=True); Mss=solve(Eq(k-g*M,0),M)[0]; result=(Mss==k/g)"},
  {"claim":"Mss = 40 for k=20, gamma=0.5", "code":"val=20/0.5; result=(val==40)"},
  {"claim":"Flux dimensional consistency: Mss units molecules when k in molecules/min, gamma in 1/min", "code":"k=20; g=Rational(1,2); result=(k/g==40)"}
]