Lecture 2 Flashcards
How does one minimize 1,3 Allylic Strain?
If possible, place 2 hydrogens in the coplanar positions across the 1,3 carbons. If 2 hydrogens are not available, then simply place the 2 smallest groups in these positions.
How does one minimize 1,3 Allylic Strain in a peptide?
Draw the peptide (or build it) with the double bond between the Nitrogen and Carbon (negative charge on O), then place the hydrogen on the alpha carbon in the coplanar position with the O-
How does one draw the lowest energy conformation of a peptide?
Orient the R groups in their lowest energy conformations (when necessary)
Why do peptide bonds favor the trans configuration over the cis?
In cis conformation, there is poor overlap between the P orbitals on the O, C and N, which translates to that conformation requiring a large amount of energy to form (high energy transition state) and an unstable transition state. As a result, there is a high kinetic barrier to isomerization
Primary peptide structure
Linear sequence of AAs
Secondary peptide structure
alpha helix or beta pleated sheet
Tertiary peptide structure
Folding of single peptide chain into 3D conformation
Quaternary peptide structure
Association of multiple tertiary structures with one another to form protein complexes
Where are the R groups in a beta pleated sheet?
Extend perpindicular to the plane of the sheet and alternate pointing up and down
What pattern in an AA sequence would one expect to see if the 2’ structure of the peptide will be beta pleated sheet?
Alternate between polar and non-polar
What gives rise to alpha helix 2’ structure?
Hydrogen bonding between backbone atoms approximately 2 amino acids away from one another
Where are the R groups in an alpha helix?
Radiate outward from helix
Where are the carbonyls in an alpha helix? What does this result in with regards to charge of helix?
All point in same direction (either up or down). Creates one end of the helix that is more charged than the other
What pattern in an AA sequence would one expect to see if the 2’ structure of the peptide will be alpha helix?
i, i+4 (or i+3), and i+7 AAs are all polar or all non-polar
What drives the folding of proteins?
The hydrophobic effect - an unfolded protein causes ordering of water molecules around hydrophobic residues b/c water can only interact with itself and not the hyrophobic residues. This creates a high degree of order amongst water molecules at the solvent layer around the peptide. However, when those hydrophobic residues are folded on the inside of the protein and water is allowed to interact with polar residues on the outside of the protein instead, the water can interact with more than just itself so the water can take on a more disordered state and has more possible interaction states. This is entropically favorable and is the driving force of the folding of proteins.