chapter 6 section 1

Question 1

Where do hydrogen bonds typically form in proteins?

Answer 1

Between peptide backbone atoms and between H-bond-capable side chains, often on the protein surface or in the interior.

Question 2

How does environment affect hydrogen bond strength?

Answer 2

H bonds in the protein interior are stronger than those exposed to water

Question 3

How much energy does a single hydrogen bond contribute?

Answer 3

A few kJ/mol, but collectively they strongly stabilize protein structure.

Question 4

What is the role of hydrogen bonds in α-helices?

Answer 4

Every interior residue’s C=O and N–H groups form hydrogen bonds along the helix.

Question 5

Why are hydrogen bonds important for proteins?

Answer 5

they are essential for maintaining 3D structure and stability.

Question 6

What drives hydrophobic interactions in proteins?

Answer 6

Nonpolar side chains cluster together to avoid water, minimizing unfavorable interactions.

Question 7

Are hydrophobic interactions enthalpy- or entropy-driven?

Answer 7

Entropy-driven; clustering of nonpolar residues increases the disorder of surrounding water.

Question 8

Where are hydrophobic amino acids usually located in proteins?

Answer 8

In the interior/core of the protein.

Question 9

Where are polar amino acids usually found in proteins?

Answer 9

On the protein surface, interacting with water or other polar groups.

Question 10

What is the principal force driving protein folding?

Answer 10

Hydrophobic interactions among nonpolar residues

Question 11

What causes ionic interactions in proteins?

Answer 11

electrostatic attractions between opposite charges or repulsions between like charges

Question 12

Which amino acids commonly carry positive charges?

Answer 12

Lysine, arginine, and histidine

Question 13

Which amino acids commonly carry negative charges?

Answer 13

Aspartate and glutamate.

Question 14

Where do ionic interactions usually occur in proteins?

Answer 14

On the protein surface, where charged residues interact with water

Question 15

Why are ionized residues unfavorable in the hydrophobic core?

Answer 15

The core is nonpolar, making ionized residues energetically unstable there

Question 16

How can salts like NaCl affect ionic interactions?

Answer 16

They compete for charged sites, weakening electrostatic interactions between residues.

Question 17

What are van der Waals interactions?

Answer 17

Weak attractive or repulsive forces between nonbonded atoms due to instantaneous dipole-induced dipole effects

Question 17

Are surface ionic interactions important?

Answer 17

yes, they contribute to protein stability.

Question 18

How strong are individual van der Waals interactions?

Answer 18

About 0.4 to 4.0 kJ/mol

Question 19

Why are van der Waals interactions important in proteins?

Answer 19

provides the cumulative weak attractive forces that stabilize the protein

Question 20

Are van der Waals forces attractive, repulsive, or both?

Answer 20

Both; attraction dominates at optimal distances, repulsion occurs if atoms are too close.