Lecture 6 Flashcards
State the 3 Non-covalent interactions that govern protein folding stability
Van der Waals interactions (short range repulsion)
Hydrogen Bonds
Electrostatic Forces (ex. ion pairs and salt bridges)
Describe Hydrophobic interactions that govern protein folding stability
Nonpolar groups do not interact favorably with water, therefore the bonds they form are primarily due to their exclusion from water
The hydrophobic interaction is a major factor in the ____ and stability of hydrophobic interactions in proteins
folding
Hydrogen Bonds are much _____ than covalent bonds (has to do with the strength of the bond). Give a reason why this is the case.
Weaker
Hydrogen bonds are 1 A longer than covalent bonds
State 3 possible Hydrogen Bonds
N-H
O-H
F-H
Name the 4 determinants of folding
Secondary Structure
Hierarchical folding
Hydrophobic Effect
Context dependent
Alpha-helix structures are stabilized by intrachain ______ bonds between which groups?
Hydrogen
between NH and C=O groups
Compare “right handed” and “left handed” alpha helix structures in terms of clockwise or counter-clockwise. Which of these structures is found in proteins?
Right handed = clock-wise
left handed = counter clock wise
alpha-helices in proteins are right-handed
Beta-sheets are stabilized by hydrogen bonding between what?
polypeptide strands
Describe what the structure of Beta-sheets are composed of AND what interaction binds them together
Beta-sheets are composed of 2 or more beta strands that are fully extended and are linked together via hydrogen bonds
True or False:
Beta sheets can run in either a parallel direction or in an antiparallel direction. explain.
True
Give the 3 names that describe the beta-sheet structure’s turn in order to form compact and globular shapes for a polypeptide chain
Reverse turn
Beta-turn
Hairpin turn
What are the groups that form hydrogen bonds that provide stability for beta sheet proteins?
C=O and NH groups
True or False:
Omega loops only participate in protein-protein interactions. explain.
False
Omega loops participate in both protein-protein interactions AND interactions with other molecules as well
State the characteristic structure and type of interactions that form superhelix, Alpha-helical coiled coil. (alpha-keratin)
Characterized by a central region of 300 AA’s that contains Heptad repeats (allows 2 alpha-helices to interact with one another)
The 2 helices that come together to form the superhelix alpha-keratin, associate with one another via weak interactions (Van der Waals forces and Ionic interactions)
Describe what is unique about the structure of Bovine insulin (2 things)
the alpha-chain has an intra-chain disulfide bond AND the 2 chains that form the structure of bovine insulin are linked by interchain disulfide bonds
Explain the steps that are described by the “folding funnel” that describes the entropy and energy level associated with a folding protein
- rapid formation of secondary structure
- formation of domains through cooperative aggregation (“folding nuclei” concept)
- Formation of assembled domains (“molten globule” concept)
- Adjustment of Conformation
- A more rigid structure is formed (finishing touches)
In Calmodulin, a Ca2+ sensing molecule, how many repeating motifs are present and why are these useful?
it has 4 repeating motifs and they are useful bc each motif can bind to a Ca2+ ion (it can bind to a maximum of 4 of these ions)
Describe the concept of “context-dependent” conformations of a peptide sequence
When the exact same peptide chain can take on alternative conformations, depending on the protein it is currently a part of
ex. VDLLKN exists as an alpha helix in one protein and a beta-strand in another
Describe the 2 context-dependent conformations of Lymphotactin and which of these is more prevalent
Lymphotactin can exist as a chemokine structure or as a Glycosaminoglycan-binding structure
(TRICK) These conformations exist in equilibrium
Describe the structure of the Molten Globule State
Molten Globule State: an intermediate conformational state between the native and the fully unfolded states of a globular protein
(basically has pants on, but isn’t wearing a belt ; half ready, half chilling)
State the 5 specific characteristics of the Molten Globule State of a protein
- the presence of a “native-like” content of secondary structure
- The absence of a specific tertiary structure produced by the tight packing of AA side chains
- Compactness in the overall shape of the protein molecule, with a radius 10-30% larger than that of the native state
- The presence of a loosely packed hydrophobic core that increases the hydrophobic surface area accessible to the solvent
- It is not specific and occurs in the early state of protein folding
Describe the globule and molten side chain portions of the molten globule state of a protein (be sure to include how this structure is stabilized)
The globule is compact
The molten side chain structure is primarily stabilized by nonspecific hydrophobic interactions