3D protein structure

Question 1

What type of reaction forms a peptide bond?

Answer 1

Condensation (dehydration)

Question 2

What type of reaction will break a peptide bond?

Answer 2

Hydrolysis

Question 3

Which two modifications can be made to the N-terminus in a protein?

Answer 3

Acetyl or formyl

Question 4

Which two modifications can be made to the C-terminus in a protein?

Answer 4

Ester or amide

Question 5

How can a modification to the C or N terminus affect the pKa of a protein?

Answer 5

The modification causes the protein to lose an ionizable group

Question 6

What is the native conformation?

Answer 6

The functional conformation that is the most stable with the maximum amount of non-covalent interactions

Question 7

Is the native conformation far more stable than the unfolded protein?

Answer 7

No, H-bonds don’t contribute too much to stability

Question 8

What drives protein folding?

Answer 8

Hydrophobic interactions that decrease the entropy of the protein and increase the entropy of the surrounding water

Question 9

Are disulfide bonds found in every protein?

Answer 9

No, most intracellular proteins don’t have any

Question 10

Why can’t disulfide bonds form inside a cell?

Answer 10

Reducing environment

Question 11

What organisms have disulfide bonds in intracellular proteins?

Answer 11

Thermophilic bacteria and archaea, keeps the proteins from denaturing at high temperatures

Question 12

Which non-covalent interactions contribute to protein stability?

Answer 12

Van der Waals, H bonds, ionic interactions, hydrophobic interactions

Question 13

Which non-covalent interaction makes a huge energy contribution to protein stability?

Answer 13

Hydrophobic interactions

Question 14

Which amino acid side chains are H bond donors?

Answer 14

S, T, Y, R, C, K, Q, N, E (HA), D (HA), H, W, backbone NH

Question 15

Which amino acid side chains are H bond acceptors?

Answer 15

S, T, Y, R (A-), K (A-), Q, N, D, E, H (A-), backbone C=O

Question 16

Why don’t H bonds contribute much energy to protein stability?

Answer 16

Folding requires the H bonds with the water to be broken, so the groups aren’t much happier once folded

Question 17

What is the hydrophobic effect?

Answer 17

Tendency of hydrophobic groups to aggregate together to hide from the polar environment

Question 18

What are the two rules of protein structure?

Answer 18

Maximize number of H-bonds and ionic interactions (DeltaH)

Minimize exposure of hydrophobic groups to water (DeltaS)

Question 19

Why are there limits to what shape a protein can fold into?

Answer 19

Peptide bonds can’t rotate
Steric interference between main chain and side chains
Proline

Question 20

Which bond is between the Alpha carbon and the NH of the peptide backbone?

Answer 20

Phi

Question 21

Which bond is between the alpha carbon and the CO of the backbone?

Answer 21

Psi

Question 22

What type of angles are Phi and Psi in?

Answer 22

Dihedral/torsion

Question 23

What type of plot shows the allowed combinations of Phi and Psi angles?

Answer 23

Ramachandran plot

Question 24

Which two amino acids have a Ramachandran plot that is different from the other amino acids? Why?

Answer 24

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