Lecture 5: Structure of Proteins Flashcards
A functional protein is in its
native state
Do any of the 4 intermolecular forces predominate in protein folding?
No, every protein is different
What does resonance cause in the primary chain
to be quite rigid and nearly planar
What is the phi angle?
What is the psi angle?
angle around the a carbon - amide nitrogen bond
angle around the a carbon - carbonyl carbon bond
Why are some psi and phi angle unfavorable?
Because of steric crowding of backbone atoms with other atoms in the backbone or side chains
When are some psi and phi angles more favorable?
Because of chance to form favorable H-bonding interactions along the backbone
What are the blacked out areas
What are the two common secondary structures?
a helix and b sheet
What is a random coil
Irregular arrangement of polypeptide chain (not misfolded)
What are some characteristics of an alpha helix
- Helical backbone is held together by hydrogen bonds between the backbone amides of an n and carboxyl group of an n+4 amino acids
- All are right-handed helix with 3.6 residues (5.4 A) per turn
- Side chains point out and are roughly perpendicular with the helical axis
What is the inner diameter of an alpha helix and outer diameter?
Inner: 4 - 5 A
Outer: 10-12 A
What type of sequences affect helix stability
- Small hydrophobic residues such as Ala and Leu are strong helix formers
- Pro acts as a helix breaker because the rotation around the N-C angle is impossible
- Gly acts as a helix breaker because the tiny R group supports other confirmations
- Attractive or repulsive interactions between side chains 3 to 4 amino acids apart will affect formation
- Two aromatic amino acids residues are often space 3 to 4 amino acid for hydrophobic interactions
The alpha helix has a large macroscopic dipole moment. Where do negative charged residues often occur?
Near the positive end of the helix dipole. This is a favorable interaction and help stabilize
Why do beta sheets occur and some characteristics?
- Due to planarity of the peptide bond and tetrahedral geometry of the alpha carbon
- Sheets are held together by the hydrogen bonding of amide and carbonyl groups of the peptide bond from opposite strands
- Side chains protrude from the sheet, alternating in an up-and-down direction
What are the two directions of the B sheets
Parallel: strands that are oriented in the same direction
Antiparallel: strands that are oriented in the opposite directions