3 - Peptide Bond Properties and Conformation Flashcards
(34 cards)
What is one of the major driving forces for protein folding?
The hydrophobic effect
How does the hydrophobic effect contribute to protein folding?
Proteins fold to remove nonpolar side chains from contact with water
True or false: hydrophilic side chains can never be found in the interior of a protein
False: they can be found in the active site for reactivity
What is the hydrophobic effect?
The tendency of non-polar solutes to prefer a non-aqueous environment
What is the enthalpic cost of not following the hydrophobic effect?
This breaks H-bonds and looses the orientation of the “ice crystal” structure, decreasing enthalpy
What is the entropic cost of not following the hydrophobic effect?
The system is more constrained and ordered, so entropy is decreased
How is the hydrophobic effect important in protein-drug interactions?
Desolvation to strip water off of the molecule
What rule of thumb is used for the hydrophobic effect?
Burial of 1 A^2 of hydrophobic surface is 20 cal/mol @ 298K
What is ionization state of an amino acid dependent on?
The surrounding environment
What pKa values are generally given?
Solution pKa values
True or false: pKa values in a protein match solution pKa values
False: a protein can modulate the environment to shift pKa
What is pI?
The pH where the protein has no net charge
What are the pKa’s of Thr and Ser?
Much higher than possible physiological pH values
If an Asp is next to a negative group, will the pKa go up or down and why?
Asp wants to stay prot (bad electrostatics), Ka decreases, pKa increases (less acidic)
If an Asp is next to a positive group, will the pKa go up or down and why?
Asp wants to deprot (good electrostatics), Ka increases, pKa decreases (more acidic)
If an Asp is in a hydrophobic core, will the pKa go up or down and why?
Asp wants to stay prot (hydrophobic effect), Ka decreases, pKa increases (less acidic)
If an Asp is on the surface, will the pKa go up or down and why?
Asp wants to deprot (H-bonds), Ka increases, pKa decreases (more acidic)
What can increase how well water can stabilize charge?
Add salts (mM range)
Which is better for stabilization: water, or the peptide backbone?
Water (stronger dipoles)
If Lys is to act as a base, what can you say about its structure?
It is deprot
If pH > pI, what is the net charge on the protein?
Negative
If pH < pI, what is the net charge on the protein?
Positive
When are folded proteins usually less soluble?
At pH = pI (no net charge)
Which amino acids absorb light at 280 nm?
Trp, Tyr, and Phe (aromatic)
