Ch. 6 Flashcards
(64 cards)
Angle between Nitrogen and alpha Carbon
Phi (Φ)
Angle between alpha carbon and carbonyl carbon
Psi (Ψ)
What is the shaded area of a Ramachandran plot
most favorable Φ and Ψ angles
What are the 3 secondary structures
α-helix, β-sheets, and turns and cross overs
How are α-helices stabilized
Backbone stabilized by H-bonds spaced 4 residues apart
Residues per turn in an α-helix
3.6
Most common orientation of α-helices in nature
right handed (Φ=-60, Ψ=-50)
What effect do side chains have in an α-helix
Determines solubility in water
What amino acids can be considered helix breakers
Proline and Glycine
How are β-sheets stabilized
Backbone is stabilized by H-bonding between separate β-strands
What are β-strands composed of
tight α-helix with 2 residues per turn
Orientation of R groups in β-strands
180 apart
3 types of β-sheets
parallel (N-terminals start at same sport), anti-parallel, and mixed (both parallel and anti-parallel)
3 ways to change direction
Proline, β-turn, and cross over
What conformation around the peptide bond allows proline to have a natural turn
cis conformation
How to form β-turn
H-bond between carbonyl oxygen of a residue with the amide proton of another residue 3 AA away
Favored AAs in β-turns
Glycine (less sterics) and Proline (natural curve)
What is a cross over
short α-helical segment that connects β-strands
Two types of Fibrous proteins
keratin (hair and nails) and collagen (skin, bones, tendons, blood vessels)
Structure of the initial monomer in keratin
central right handed α-helix (rod domain)
two initial keratin monomers form a dimer called
left handed coiled coil
Why do coiled coils form
red domain is composed of heptad repeats that create a non-polar strip on the outside of the helix (hydrophobic effect)
Two coiled coils associate to form?
protofilament
Two protofilaments associate to from?
right handed protofibril
