Ch. 4 The 3D Structure of Proteins (E2) Flashcards
What is the key difference between a standard polypeptide and a functional protein in terms of their number of conformations?
Standard polypeptide - many conformations
Functional protein - unique 3D structure; very few stable conformations
A functional protein is usually in the {…} energy state.
Lowest
A functional protein is said to be in its {…} structure.
Native
What helps fold a protein into its native conformation?
A network of weak interactions (ionic, H-bond, hydrophobic, Van der Waals)
What is the only type of covalent bond that contributes to folding a protein into its native conformation?
Disulfide bond (S-S)
Given that a functional protein is thermodynamically stable (and even spontaneous & favored), what can be said about the its free energy state?
ΔG < 0
Where will you find polar & charged amino acids on a folded protein? Additionally, what types of interactions will you see with polar & charged groups, respectively?
On the surface
Polar: H-bonding
Charged: ionic
(S, T, N, Q, D, E, K, R)
Where will you find charged amino acids, specifically, on a folded protein?
Close to oppositely charged groups
(D/E close to K/R)
Where will you find hydrophobic amino acids on a folded protein?
On the inside of the fold along the hydrophobic pocket
(F, Y, W, A, V, L, I, P, M)
What are the 2 key (simple) rules for most structural protein pattern mentioned in this chapter?
1) Hydrophobic residues are tucked away from water in hydrophobic pocket
2) # of H-bonds & ionic interactions is maximized to reduce # of unpaired H-bonding & ionic groups
What are the 2 main dihedral angles?
ϕ (phi) & ψ (psi)
What do dihedral (torsion) angles reflect?
Rotation about each of the 3 repeating bonds in a peptide backbone
The important dihedral angles in a peptide are defined by the three bond vectors connecting four consecutive main-chain (peptide backbone) atoms. What are these 4-element bond chains for ϕ & ψ angles?
Phi: C-N-Ca-C
Psi: N-Ca-C-N
Which bond does rotation occur in a phi torsion angle?
N-Ca bond
By what angle are phi and psi angles defined when a polypeptide is fully extended and all peptide groups are in the same plane?
+/- 180 degrees
Under what condition would some phi & psi combinations be unfavorable?
Steric hindrance/crowding between backbone atoms or side-chains
Under what condition would some phi & psi combinations be favorable?
The chance to form favorable H-bonding interactions along the backbone
What information does a Ramachandran plot tell about the phi & psi dihedral angles in a protein?
The Ramachandran plot displays their distribution
What other 2 key pieces of information does a Ramachandran plot show?
1) Common secondary structure elements
2) Regions w/ unusual backbone structure
What are the 2 regular arrangements of a secondary structure? Explain how they differ in terms of their H-bond stabilization.
1) α helix: H-bonds between nearby residues
2) β sheet: H-bonds between adjacent segments that may not be nearby
This is an irregular arrangement of the polypeptide chain.
What is a random coil?
Is an α helix typically right-handed or left-handed?
Right-handed
Which way do the side chains face on an α helix? Inside or outside?
Outside
An α helix will frequently prefer Ala to which 4 amino acids?
Arg, Leu, Lys, & Met
