Secondary, tertiary and quaternary structures (Dr.Miles TAMU)

Question 1

Hydrogen bonds in proteins structure

Answer 1

the components the peptide backbone tend to form H-bonds with one another. Each hydrogen will contribute 12kJ/mol of stabilization energy

Question 2

Hydrophobic Interactions in proteins structure

Answer 2

This clustering in entropy driven and will also cluster in nonpolar environments
- almost al side chains are nonpolar

Question 3

Electrostatic Interactions in proteins structure

Answer 3

Almost always located on the surface of the protein and interact with the solvent water molecules and salts

Question 4

Dipole-Induced Dipole Interactions in proteins structure

Answer 4

accounts for 0.1-4 Kj/mol of stabilization

Question 5

What amino acid can have both cis and trans with steric strain

Answer 5

Proline

Question 6

Psi bond location

Answer 6

rotation around Ca-C bond

Question 7

phi Bond location

Answer 7

Rotation around Cn-C bond

Question 8

Alpha-helix residues n and p

Answer 8

n= 3.6
p= 5.4

Question 9

what are the 5 constraints that effect stability

Answer 9

1.) Electrostatic repulsion or attraction of successive amino acid residues with charged side chains destabilize the alpha Helix.
2.) Successive bulky amino acids destabilize the alpha Helix.
3.) The interactions of amino acids spaced three residues apart have a great effect the stability of the
alpha Helix.
4.) The occurrence of proline or glycine residues destabilizes the helix.
- Proline is cyclic and rigid.
- It produces a kink in the helix. The alpha amino nitrogen atom is part of the rigid ring and
cannot participate in the back bone hydrogen bonding.
- Glycine has too much conformational flexibility.
5.) The interaction between amino acid residues at, the ends of the helix that interact with the dipole
moment inherent of the alphahelix effect the stability of the helix.
- Negatively charged amino acids at the N-terminal stabilize the helix. Positively charged
amino acids at the C-terminal end stabilize the helix by charge-dipole interactions.
The

Question 10

3^10 helix n and p

Answer 10

n=3
p=6

Question 11

Antiparallel beta pleated sheet n and p, and what is is

Answer 11

n=2
p=7
Is the fundamental structure of silk and is completely streached

Question 12

Parallel beta sheets n and p

Answer 12

n=2
p= 6.5