Questions to think about before class meetings
1. Suppose you have a protein that reads the DNA sequence shown below and you wish to reverse the direction of the protein on the DNA but still have it bind on the same face of the DNA (with respect to surrounding sequence and protein binding sites 10 or more bases away). There are two ways to think about this. You can (conceptually) cut both strands of the DNA on both sides, rotate the segment containing the sequence by 180 degrees, and rejoin the strands. If the rotation is about an axis perpendicular to the paper, it appears to leave the DNA sequence on the same face of the DNA. If the rotation is about an axis in the plane of the paper (and perpendicular to the axis of the DNA), it appears to move the DNA sequence to the opposite face. Both cut, rotate, and join schemes ought to give the same result, but they appear not to. What is going on here?
2. Chemists and biochemistry texts and lecturers say that the peptide bond is not freely rotatable. Just how stiff is it? How would you want to understand its stiffness in a way that helps you understand protein structure and function?
3. Design (in principle) an efficient, sensitive, practical, biosensor for the presence of mercury ions.
4. Weather is chaotic, see butterfly effect, but is a protein molecule immersed in a bath of 100,000 water molecules and simulated by a molecular dynamics program deterministic or chaotic? Devise a method for determining the answer.