Agbas Review Flashcards
(51 cards)
2 types of interactions that govern protein folding stability
Non-covalent and hydrophobic
What are considered determinants of protein folding
Secondary structure, hierarchical folding, hydrophobic effect, context depending
How are alpha helix stabalized
Intrachain hydrogen bonds
In alpha helices what occurs between NH and C=O groups
Hydrogen bonds which stabilizes the helix
Where do the H bonds take place in an alpha helices
4 amino acid residues ahead in the sequence
How do amino acid residue relate to the next one in the chain
A rise of 1.5 A along the helix axis, 100 degrees rotation, 3.6 amino acid residues per turn
Which direction are most helices turning in nature
Right handed, it is more energetically favorable
How are beta sheets stabilized
H bonding between polypeptide strands
What are beta sheets composed of
2 or more polypeptide strands called beta strands which are fully extended
What is the distance between adjacent amino acids along a beta-strand
3.5 angstroms
Which protein folding motif can be found running parallel and antiparallel directions
Beta sheets
What is a reversal in direction in the structure of the protein called
Reverse turn, beta-turn, hairpin turn
T/F Loops have a regular periodic structure
False, loops do not have a regular periodic structure
What are 4 characteristics of polypeptide loops
Often well defined and rigid, Positioned on the surface of the protein, participates in protein-protein interactions, participates in interactions with other molecules
What is the timeline of proteins entering a folding funnel
- Rapid formation of secondary structure
- Formation of domains through cooperative aggregation
- Formation of assembled domains (molten globule)
- Adjustment of conformation
- More rigid structure
Characteristics of Molten Globule state
- Presence of a native-like content of secondary structure
- The absence of a specific tertiary structure produced by the tight packing of amino acid side chains
- Compactness in the overall shape of the protein molecule, with a radios 10-30% larger than that of the native state
- The presence of a loosely packed hydrophobic surface area accessible to solvent
- It is no specific and occurs in early stage of protein folding
What is the function of protein disulfide isomerase
Rearranges the polypeptide non-native S-S bonds
T/F Molten Globule stage is intermediate and very short
True
T/F Partially loss of folding stabilizes the remainder of the structure
False, destabilized
T/F Protein folding can be partially completed
False, it is an all or nothing process
What is the function of HSP 70
Driven by ATP: Reverses misfolds, newly synthesized proteins, unfold/refold of trafficked proteins
What is a molecular chaperone
Essential protein that binds to unfolded and partially folded polypeptide chains
What does a molecular chaperone prevent
Improper association of exposed hydrophobic segments, non-native folding, polypeptide aggregation and precipitation
What does molecular chaperone allow
Misfolded proteins to refold into native confirmation
