Solution

ID: past-exam-of-the-biological-physics-course-of-the-university-of-oxford/2017/3/a/solution

In spectrin unfolding by force spectroscopy, the cantilever measures tension through its calibrated deflection, while displacement of the pulling point increases the separation of the protein attachments. The protein extension is obtained after allowing for cantilever compliance and any linker extension; it is not simply the commanded displacement.
A folded spectrin repeat stores much of its backbone in a compact domain. Between unfolding events, the already released chain is stretched: increasingly straight conformations have fewer accessible configurations, and the resisting entropic force rises nonlinearly. A peak is reached when a still-folded domain crosses an unfolding barrier on the timescale of the imposed loading. Its released backbone increases the available contour length abruptly. At nearly the same end-to-end distance the fractional extension is then smaller, so tension drops. Pulling resumes on the next, longer-chain elastic branch. Repeated release of domains produces the saw-tooth sequence.
The record is therefore evidence for sequential mechanical unfolding of modular structure, not repeated stretching of a fixed-length rod. For the nominal eight-domain construct, successive branches correspond to increasing numbers of unfolded repeats. The order and rupture forces can fluctuate because barrier crossing is thermally activated and depends on loading rate, structural heterogeneity and pulling geometry; equivalent repeats need not rupture at identical force.
The horizontal separation between worm-like-chain fits at the same force estimates the added contour length, whereas the vertical force drop at one extension reflects redistribution of tension. These are distinct measurements. A repeat increment near the specified is consistent with repeated similar structural units. The gain is a net release relative to the folded span and attachment geometry; is not automatically the universal contour length of a peptide residue.
During unloading, relaxation and possible refolding can restore compact domains. Hysteresis would indicate dissipative or kinetically delayed processes. Neither the peak force alone nor an arbitrary saw-tooth area directly equals an equilibrium unfolding free energy: one must separate chain elasticity, cantilever storage, irreversible loss and pulling-rate effects. The worm-like-chain branches describe released-chain elasticity, not the molecular transition state responsible for a rupture peak.

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