Chapter 4: Protein structure Flashcards
Native fold
When protein molecules adopt a a specific 3D conformation based on the amino acid sequence
What does dynamic & marginally stable means?
Protein biological function depends on its 3d structure
The ______ 3D structure has the lowest energy with the maximum number of weak interactions
Native
What are the four levels of protein structure?
- Primary structure
- Secondary structure
- Tertiary structure
- Quaternary structure
What are the favorable interactions among proteins?
- Hydrophobic effect
- Hydrogen bonds between protein hydrogen bond donors and acceptors
- London dispersion
- Electrostatic interactions
Hydrophobic effect (predominant stabilizing force)
Clustered nonpolar groups form a hydrophobic core reducing highly ordered water shells
Hydrogen bonds between protein hydrogen bond donor & acceptors
Interactions with N & O to form hydrogen bonds along the peptide chain forms regular stable structures
London dispersion forces
Weak attraction between atoms contributes significant stability in protein’s interior
Electrostatic interactions
Strong interactions between permanently charged groups such as salt-bridges
Peptide group is what?
6 atoms that occupy the same plane
___________ character restricts conformation in either trans or cis configuration
Partial bond
___________ from backbone & R groups size/ limit a peptide formation
Partial bond
Most proteins peptide groups are _______ conformations to minimize steric conflict
trans
____________ plots show the distribution of the phi & psi angles
Ramachandran
What are the conformation angles in common secondary structures
- Beta sheets
- Alpha helix
- Collagen helix
- Left-handed alpha helix
