Molecular + cell biology¶

What you will develop¶

Model cells as chemical, energetic, informational and mechanical systems; understand membranes, metabolism, signaling, division and gene expression.

Before you begin¶

Recorded prerequisites:

Study and practice¶

Progress by the work you can do, not by a fixed calendar.

Practice sequence 32¶

Spine: OpenStax Biology 2e

Reading: Ch. 4 cell structure + Ch. 5 membranes and transport

Know: Understand compartments, membranes, transport, electrochemical gradients and organelle functions.

Reconstruct: Reconstruct diffusion/osmosis/active-transport driving forces and membrane area/volume scaling.

Do: Model nutrient/oxygen diffusion into a cell/tissue sphere and identify size limits without vasculature.

Defend: Why does surface-area-to-volume scaling constrain artificial tissue?

Gate: Pass: transport limitation predicted before simulation and tied to geometry.

Source: source

Practice sequence 33¶

Spine: OpenStax Biology 2e

Reading: Ch. 6 metabolism + Ch. 7 cellular respiration + Ch. 8 photosynthesis

Know: Track biological energy, redox carriers, ATP and metabolic pathways as controlled reaction networks.

Reconstruct: Derive ATP/free-energy coupling and proton-gradient/chemiosmosis logic.

Do: Create stoichiometric energy/redox balance for a simplified microbial bioreactor or photosynthetic system.

Defend: How is metabolism simultaneously chemistry, thermodynamics and control?

Gate: Pass: carbon/electron/energy balances close.

Source: source

Practice sequence 34¶

Spine: OpenStax Biology 2e

Reading: Ch. 9 cell communication + Ch. 10 cell cycle/division

Know: Understand receptors, signaling cascades, feedback, proliferation checkpoints and cell-state transitions.

Reconstruct: Draw a signaling feedback loop and derive simple Hill-function response; reconstruct cell-cycle checkpoint logic.

Do: Simulate a bistable cell-fate switch and test sensitivity to signaling noise.

Defend: Why can the same signal cause different outcomes in different cells?

Gate: Pass: mechanism includes receptor/state/context, not signal name alone.

Source: source

Practice sequence 35¶

Spine: OpenStax Biology 2e

Reading: Ch. 14 DNA replication/repair + Ch. 15 transcription/translation

Know: Understand information storage, replication fidelity, transcription, translation and mutation sources.

Reconstruct: Reconstruct central dogma with directionality/enzymes and simple error-rate compounding.

Do: Model information fidelity across replication and protein expression; calculate mutation/error burden across many generations.

Defend: Where does biological 'error correction' occur and where is error intentionally retained?

Gate: Pass: distinguish DNA mutation, transcription error and translation error consequences.

Source: source

Practice sequence 36¶

Spine: OpenStax Biology 2e

Reading: Ch. 16 gene regulation + Ch. 17 biotechnology/genomics

Know: Understand gene regulation, PCR/sequencing/editing concepts, biotechnology workflows and measurement limitations.

Reconstruct: Reconstruct lac-style regulatory logic and PCR amplification scaling.

Do: Design a non-clinical synthetic gene-circuit experiment in simulation: sensor -> regulator -> reporter with controls and failure modes.

Defend: Why is successful editing not equivalent to safe/functional phenotype?

Gate: Module defense: biological intervention -> mechanism -> measurement -> controls -> off-target/selection risks.

Source: source

Exit gate¶

Closed-book: 120 min: membrane transport, energy/redox, signaling, cell cycle, DNA replication/expression/regulation.

Novel problem: Model a cell/tissue/bioreactor intervention and specify what measurements establish function rather than mere presence.

Artifact: Transport/metabolic/gene-circuit simulation with controls.

Defend: Defend mechanism, cell-state context, measurement, off-target/selection and scaling limits.

Pass criterion: Pass if mass/energy/information balances and control logic are mutually consistent.

Transfer problems¶

Try these before consulting solutions or asking for the complete answer.

Membrane: Predict direction of water/solute movement across a selective membrane.
Transport: Estimate maximum viable tissue thickness from diffusion/consumption.
Metabolism: Balance carbon/electrons/ATP in a simplified pathway.
Chemiosmosis: Explain how a proton gradient couples transport to ATP synthesis.
Signaling: Model receptor-response saturation and feedback.
Cell cycle: Map a checkpoint failure to uncontrolled proliferation risk.
Replication: Estimate mutation burden after many replications given error/repair rates.
Expression: Translate a DNA sequence toy example into RNA/protein and identify possible regulation points.
Gene regulation: Model inducible expression with Hill function and leakiness.
Biotech assay: Design positive/negative/process controls for a gene-editing measurement without performing real editing.