Protein Folding Flashcards
the core structure of amino acid includes the ___ group, the ____ group, ___ and the ___ ___ attached to a central carbon
amino, carboxyl, H, side chain
The most common conformation of amino acid is the ____ form at pH7, with ___ and ___
zwitterion, NH3, COO-
a peptide bond is ___ and cannot rotate but there is rotation around the __ ___. The ___ __ has limited freedom of rotation
planar, alpha carbon, polypeptide backbone
Ionic interactions in a protein are ___ range interactions from ____A. The strength of the interaction ____ over distance. Atoms of the same charge leads to _____ which can also contribute to protein structure
long, 2.4-4.0, decreases, repulsion
Hydrogens attached to ___, ___ or ___ can participate in H-bonding. For proteins the most common H bonding occurs with ___ and ___. The most common distance for H bonds are ____A
N, O, F, N-H, O-H, 2.6-3.2
hydrophobic interactions in proteins are driven by ___.
entropy
alpha helices have residues ___ amino acids away that are compatible for interaction. __ is rarely found due to it’s flexibility and ___ is rarely found due to its rigidity. There is a net ____ in the helix, so electronegative amino acids are preferred at the ___ terminus
3-4, glycine, proline, N
The tertiary structure involves amino acids that are very ___ from one another. They are highly driven by ___ interactions.
distant, hydrophobic
the __ ___ of the protein is the most stable when compared to folding intermediates or ____ ___ states
native conformation, partially folded__
___ ___ and __ ___ are very stable structures and can cause problems within the cell
amorphous aggregates and amyloid fibrils
As the nascent protein leaves the ribosome, it starts folding and is referred to as a __ ___.
molten globule
In the native state, some domains may require a ___ partner to be stable. Generally the __ portions are inside the protein, and ___ portions are on the surface
ligand, hydrophobic, hydrophilic
Folding intermediates may have some ___ structures, and some ___ portions may be exposed. The polypeptide is ____ and ___, and there is a risk of ___ due to ___ interactions with other proteins, that can lead to insolubility
secondary, hydrophobic, unstable, flexible aggregation, hydrophobic
____ assist in folding and prevent aggregation. They often recognized exposed ___ regions of folding intermediates. ATP dependent chaperones like ___ and ____ actively promote folding, substrate binding and release with ____ cycles. ATP independent chaperones like ___ prevent aggregation by binding to hydrophobic residues.
chaperones, hydrophobic, HSP70, HSP90, ATPase, SPY
HSP70 has a ___ ___ that controls substrate binding. If ATP is bound there is no substrate binding, while if ____ is bound the substrate binding domain is exposed. The _____ co-chaperone facilitates ATP hydrolysis and substrate ____. This chaperone clamps onto short amino acid segments that are ___ preventing incorrect contacts. It is contitutively expressed in the ___ but is only expressed in the ER with ___ ___
ATPase domain, ADP, DNAJ, transfer, hydrophobic, cytosol, heat stress
