Chapter 6- Tertiary and Quaternary Structures Flashcards
the tertiary structure consists of
multiple secondary structure elements
protein is folded when it adopts ___ _____ ____
biologically relevant structure
main driving force for protein folding
hydrophobic interaction
main stabilizing forces of protein folding
- formation of a large number of H bonds
- hydrophobic interactions
- Van der Waals forces
The surface of the proteins is ______ _____
predominantly polar
The core of a protein is _____ ______ and is made via _____ ______
predominantly hydrophobic, hydrophobic interactions
N-H and C=O of the backbone must be ___ in the hydrophobic core
neutralized
Water on the surface of the protein _____ the structure
stabilize
Side chains on the surface make _____ with solvent water –> ______ __ ______
H-bonds, Layer of water
Alpha helices on the surface of a protein are typically ______
Amphipathic
Hydrophobic helices are found in the protein _____
interior
Polar helices are found _____ to the solvent
completely exposed
domains are _________ _____ _____ and are typically connected by _____ ________ _______
structurally independent units, one polypeptide segment
Identical subunits are called
homo-multimers
Non-identical subunits are called
hetero-multimers
Van der Waals interactions contribute to _____ _______
oligomer stability
oligomerization is accomplished by
- unfavorable energy changes (entropy loss due to association)
- Favorable energy changes (van der waals, H-bonds, and hydrophobic interactions)
Forces driving quaternary association
- van der waals interaction
- hydrophobic interactions ‘
- Disulfide bonds
Hydrophobic interactions in quaternary structure have a ____ _____ ____ and provide enough to _____- _______ _____
main stabilization effect, counterbalance unfavorable entropy
Structural and functional advantages driving quaternary association
- stability
- genetic economy and efficiency
- bringing catalytic sites together
- cooperativity
A functional protein is a ____ protein
stable
Proteins are only ______ _____ under physiological conditions
marginally stable
Protein structures arise from a delicate ____ ____ ____
balance between forces
The free energy of proteins is ____ which means it is ____ to go from one form to the other
low, easy
Denaturing forces
sidechain conformational entropy (proteins do not want to be constrained)
Hydrophobic interaction drives the folding of proteins through the clustering of _____ ____ ___
hydrophobic amino acids
Loss of protein structure results in loss of protein _____
function
proteins denature by altering the weak _____ _____
nonbonding forces
Denaturation methods
- high temperature
- high or low pH
- Chaotropic agents
- detergents
When protein is unfolded via heat it is _____
irreversible
when protein is denatured via chaotropic agents, the process is _____
reversible
The melting temperature is when the protein is ____ folded and ____ unfolded
50%, 50%
Alpha helices monitors CD signals at
222 nm
Proteins fold in _____ ________
prearranged pathways (Levinthal paradox)
The probability of forming contact C2 is much higher if ___ is formed than in the absence of ___
C1
Protein folding occurs on an ___ _____
energy surface (landscape theory)
Unfolding/ improper folding can lead to protein _____
aggregation
Chaperone proteins guide proteins along the proper folding pathways by
providing a protective environment
Chaperone proteins are often called
heat shock proteins
What residue pairs confer flexibility and rigidity to a peptide
Gly and Pro
Why is there little allowable rotation around the peptide bond?
the partial double bond character makes the peptide bond planar
For beta sheets, the terms parallel and anti-parallel refer to
the direction of the associated peptide strands
tertiary structure is defined as
the folding of a single polypeptide chain in three-dimensional space
Why should the core of most globular and membrane proteins consist almost entirely of alpha helix and beta sheets (not loops)
Highly polar N-H and C=O bonds of the peptide backbone must be neutralized in the hydrophobic core of the protein
How does protein affect protein stability
alters ionization states
