3D protein structure Flashcards
What type of reaction forms a peptide bond?
Condensation (dehydration)
What type of reaction will break a peptide bond?
Hydrolysis
Which two modifications can be made to the N-terminus in a protein?
Acetyl or formyl
Which two modifications can be made to the C-terminus in a protein?
Ester or amide
How can a modification to the C or N terminus affect the pKa of a protein?
The modification causes the protein to lose an ionizable group
What is the native conformation?
The functional conformation that is the most stable with the maximum amount of non-covalent interactions
Is the native conformation far more stable than the unfolded protein?
No, H-bonds don’t contribute too much to stability
What drives protein folding?
Hydrophobic interactions that decrease the entropy of the protein and increase the entropy of the surrounding water
Are disulfide bonds found in every protein?
No, most intracellular proteins don’t have any
Why can’t disulfide bonds form inside a cell?
Reducing environment
What organisms have disulfide bonds in intracellular proteins?
Thermophilic bacteria and archaea, keeps the proteins from denaturing at high temperatures
Which non-covalent interactions contribute to protein stability?
Van der Waals, H bonds, ionic interactions, hydrophobic interactions
Which non-covalent interaction makes a huge energy contribution to protein stability?
Hydrophobic interactions
Which amino acid side chains are H bond donors?
S, T, Y, R, C, K, Q, N, E (HA), D (HA), H, W, backbone NH
Which amino acid side chains are H bond acceptors?
S, T, Y, R (A-), K (A-), Q, N, D, E, H (A-), backbone C=O
Why don’t H bonds contribute much energy to protein stability?
Folding requires the H bonds with the water to be broken, so the groups aren’t much happier once folded
What is the hydrophobic effect?
Tendency of hydrophobic groups to aggregate together to hide from the polar environment
What are the two rules of protein structure?
Maximize number of H-bonds and ionic interactions (DeltaH)
Minimize exposure of hydrophobic groups to water (DeltaS)
Why are there limits to what shape a protein can fold into?
Peptide bonds can’t rotate
Steric interference between main chain and side chains
Proline
Which bond is between the Alpha carbon and the NH of the peptide backbone?
Phi
Which bond is between the alpha carbon and the CO of the backbone?
Psi
What type of angles are Phi and Psi in?
Dihedral/torsion
What type of plot shows the allowed combinations of Phi and Psi angles?
Ramachandran plot
Which two amino acids have a Ramachandran plot that is different from the other amino acids? Why?
Proline: no free rotation around the Phi bond because of the side chain, much fewer conformations
Glycine: no side chain, but many more allowed Phi and Psi angles
