lecture 3 Flashcards
1) What is the reason behind a peptide bond’s strength? What else is special about peptide bonds?
The resonance ability of the carbonyl group and the nitrogen.
The dbl bond on the C=O are longer than typical C=O bond and the C-N is shorter than typical C-N bond. Electron stabilization prevents free rotation.
2) When it comes to rotation angles, what is the name of N-C rotation and C-C rotation.
N-C= phi C-C= Psi
3) What does Ramanchandran plots show us, and why is this important? What are some exception to ramanchandrons rules: ie what rotates that normally doesn’t.
It tells us the rotation values of each amino acid. Phi and Psi values are given and these may be used to determine the proteins secondary structure. Dark green on the plot shows alpha-helices and B-sheets. There are some exceptions because some amino acids allow rotation at their peptide bond: ex= proline, glycine, very bulky AA
4) Alpha helixes- Are they right or left handed? What does pitch and rise mean? How many AA per turn?
What is it that Ala is common in alpha helices and why not Tyr or Asn? Where are Glycine and Proline usually found on alpha helices?
They are right handed.
Pitch: advance per turn, the distance each turn makes, it is .54nm
Rise: advance per AA residue, how much distance each AA makes: .15nm
Roughly 3.6 AA residues per turn.
Ala is a tiny AA and the others are too bulky.
Glycine at the ends because it has too much free rotation to be in the middle at it destabilizes it and Proline can’t hydrogen bond and it too rigid so it is found at the parts where the direction changes.
5) What is the residue length of Beta strand residue?
How are these strands stabilized? There are two ways, what are they are which is most stable and why? Where are they found on the Ramachondran plot and what type of spin do they have? What is a Beta- sandwhich?
What are loops and turns? What are reverse turns ie: Beta turns?
0.32nm
Stablilized by H bonding of adjacent strands, two ways parallel and anti-parallel, the latter is more stable because the H bonds line up perfectly between the hydrogen and the carbonyl oxygen. In parallel they don’t line up properly. Found on the upper left, haw more Psi spin (C-C).
Beta-sandwhich is when sheets form a sandwhich with a hydrophobic core and a hydrophilic outer core to interact with aqueous layer.
Loops contain hydrophilic residues and found on the surface and Turns are where residues change the direction and needed to make antiparallel beta pleated sheet.
Reverse turns are very common, connect antiparallel Beta strands that are stabilized by hydrogen bonds.
