Biochemistry & Biophysics
Protein structure and purification, exploring PDB structures, enzyme kinetics and inhibition, binding and thermodynamics, spectroscopy, structural biology, molecular simulation and research career routes.
Leads to: Biochemist
Before you start
This course builds on Molecular Biology Methods, Chemistry Fundamentals and Scientific Python. Take them first if you are new to the topic.
About this course
A mid-level course for future biochemists and biophysicists who have finished Molecular Biology Methods, Chemistry Fundamentals and Scientific Python. The first module covers proteins: the four levels of protein structure and what drives folding, planning a purification scheme and judging it with a purification table, and exploring an experimental structure in a free web viewer. The second module covers enzymes and binding: fitting Michaelis-Menten parameters to assay data, identifying the type of inhibition from fitted parameters, and estimating a dissociation constant from a binding curve and converting it to a binding free energy. The third module covers biophysical methods: choosing between circular dichroism, fluorescence and NMR, comparing X-ray crystallography with cryo-EM, understanding molecular dynamics and AlphaFold predictions at a high level, and planning a graduate-school or industry route. Python activities are fill-in-the-blank and use only the standard library. Every activity is a paper, data or web exercise: nothing here involves handling chemicals, biological material or patient samples at home. Bench work must be learned under supervision in a teaching or employer lab with institutional safety training, and these careers have real entry requirements: a bachelor's degree with real lab coursework for technician roles, and usually a PhD for independent research.
Course content
Module 1
Proteins
3 lessons · 2h 53mHow proteins are built and folded, how a protein is purified and judged with a purification table, and how to explore an experimental structure in a viewer.
- 22mProtein structureReading
Explain the four levels of protein structure, what drives folding and why folded proteins are only marginally stable.
- 1h 6mProtein purificationReading
Plan a capture, intermediate and polishing purification scheme and judge it with specific activity, yield and fold purification.
- 1h 25mExploring structuresReading
Read a Protein Data Bank entry and inspect a structure in a browser viewer, checking method, resolution and confidence.
Module 2
Enzymes and Kinetics
3 lessons · 2h 8mFit Michaelis-Menten parameters to assay data, identify inhibition types from fitted parameters, and estimate binding affinity and its free energy.
- 46mEnzyme kineticsReading
Fit Michaelis-Menten parameters Vmax and Km to initial-rate data and compute kcat.
- 57mInhibitionReading
Identify competitive, uncompetitive, noncompetitive and mixed inhibition from fitted parameters and estimate Ki.
- 25mBinding and thermodynamicsReading
Estimate a dissociation constant from binding data and convert it to a standard binding free energy.
Module 3
Biophysical Methods
4 lessons · 2h 8mChoose spectroscopy methods, compare crystallography and cryo-EM, understand molecular simulation and structure prediction, and plan a research career route.
- 1hSpectroscopy for biomoleculesReading
Choose between circular dichroism, fluorescence and NMR for questions about folding, stability and binding.
- 15mStructural biology methodsReading
Compare X-ray crystallography, cryo-EM and NMR by sample needs, size range, resolution and limits.
- 15mMolecular simulationReading
Explain at a high level how molecular dynamics works and how to read AlphaFold confidence scores.
- 38mResearch careersReading
Plan a bachelor's, master's or PhD route into biochemistry and biophysics research using official sources.