Third Year Biochemistry Notes

These notes were made for Biochem 3381 at the University of Western Ontario and cover secondary structure, quaternary structure, protein purification, and miscellaneous biochemistry techniques.

Ramchandran plots and some secondary structure

Ramchandran plots-p1

Quaternary Structure

Ramchandran plots-p4

Misc Techniques

Ramchandran plots-p2

Protein Purification

Ramchandran plots-p3

Bonus! Code in R for generating Ramchandran plots like this one: Ramchandran plot

phi <- c(value,value,value…)
psi <- c(value,value,value…)
residues <- c(“number, residue”,”number, residue”,”number, residue”…)
par(pty=”s”)
plot(x=phi, y=psi,
     xlim=c(-180,180),ylim=c(-180,180), axes=FALSE,
     main=”Your title”,
     pch=20, xlab=expression(phi),
     ylab=expression(psi), cex=1, asp=1.0)
axis(1, at=seq(-180,180,90))
axis(2, at=seq(-180,180,90))
text(phi, psi, labels=residues, cex= 0.7,pos=3)
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