Chapter 4: Proteins Flashcards
What is the difference (attraction-wise) between Alpha Helices and Beta Sheets? What is the 3 rd type of secondary structure? Describe it.
In Alpha Helices, H-bonds occur between nearby residues. With Beta sheets, H-bonds don’t have to be nearby. The strands can come
from different sequences.
Random coils – no defined shape.
Describe the 4 ‘favorable interactions’ in proteins.
Hydrophobic Effect: Release of water molecules from the structured solvation layer around the molecule as the protein folds increases
entropy.
Hydrogen Bonds: Interaction of N-H and C=O of the peptide bond leads to secondary structures.
London Dispersion: Medium-range weak attraction between all atoms contributes significantly to the stability of the inside of the protein.
Electrostatic Interactions: Long-range strong interactions between permanently charged groups as well as salt-bridges esp. buried in the
hydrophobic environment strongly stabilize the protein.
Disulfide bonds and covalent linkage also important.
What are 3 good effects of resonance in peptide bonds?
Resonance causes peptide bonds to be less reactive (like in comparison to esters), causes them to be quite rigid and planar, which is
important for predicting structures, and causes them to exhibit large dipole moments in the favored trans configuration.
What is the difference between Apoproteins/Apoenzymes and Holoproteins/Holoenzymes?
Apoprotein/Apoenzymes have no prosthetic group attached. Holoproteins/Holoenzymes have a prosthetic group attached.
Where is the Phi angle located? Where is the Psi angle located?
Phi angle is around the alpha carbon-amide nitrogen bond while the Psi angle is around the alpha carbon-carbonly carbon bond.
When are Phi/Psi angles unfavorable? Favorable?
Some are unfavorable because of steric crowding, while others are favorable because of the chance to form H-bonds along the backbone.
What holds the Alpha Helical backbone together?
Hydrogen bonds between nearby backbone amides.
Alpha helix has what handedness? What is the size of the residues?
Right handed and 3.6 residues (5.4A) per turn.
In relations to the helical axis, where are Peptide Bonds located? Side Chains?
Peptide bonds are roughly parallel to the helical axis where side chains are perpendicular and point out.
Which AAs are strong helix formers? Which are helix breakers (Why)?
Alanine and Leucine are strong helix formers.
Proline is a helix breaker (because of the inability for rotation around the N-alphaC bond. Its side chains stick out and attach to itself).
Glycine is a helix breaker because the tiny R-group supports other confirmations.
In Beta Sheets, what holds the sheet-like arrangement of the backbone?
Hydrogen bonds between the more distal backbone amides.
What is the directional relationship of H-Bonds in Antiparallel Beta Sheets? Parallel Beta Sheets?
Antiparallel are in the same direction. Parallel are in opposite directions.
Over how many AAs do Beta Turns occur? What 2 AAs are common in these turns, and in what number locations?
- Proline (position 2) and Glycine (position 3).
What stabilizes the turn? Where does it come from?
Turn is stabilized by H-bond between carbonyl oxygen and amide proton 3 residues down the sequence.
What is the Tertiary Structure?
Overall spatial arrangement of atoms in a polypeptide chain or in a protein.
