Protein Structure

Question 1

What are the four levels of protein structure?

Answer 1

1. primary
2. secondary
3. tertiary
4. quaternary

Question 2

What is the primary structure of a protein?

Answer 2

The linear amino acid sequence.

(from N terminus to C terminus)

Question 3

What is the secondary structure of a protein?

Answer 3

The folding of neighboring amino acids held via hydrogen bonds.

(Hydrogen bonds between backbone amide protons and carbonyl oxygen atoms.)

Question 4

What are the two kinds of secondary structures found in a protein?

Answer 4

1. α-helices
2. β-pleated sheets

Both are held via H bonds between the carbonyl oxygen of one amino acid and the hydrogen on the amino group of another amino acid.

Question 5

What effect does the amino acid proline have on the secondary structure of a protein?

Answer 5

Its rigid cyclic structure creates kinks in α-helices and creates turns in β-pleated sheets.

Question 6

Which kind of bonds stabilize the primary structure of a protein? Secondary structure?

Answer 6

primary: peptide (amide) bonds

Peptide bonds are a specialized form of an amide bond, that forms between the –COO– group of one amino acid and the NH₃⁺ group of another amino acid. This forms the functional group –C(O)NH–

secondary: hydrogen bonds

(intramolecular)

Question 7

What is the tertiary structure of a protein?

Answer 7

3d shape

(determined by hydrophilic and hydrophobic interactions between R groups)

Question 8

Explain the process of hydrophobic bonding that occurs in the tertiary structure of a protein.

Answer 8

Hydrophobic R groups are moved AWAY from water towards the interior of a protein.

Examples: phenylalanine, leucine, alanine, valine and isoleucine (FLAVI)

Question 9

How does a disulfide bridge (or disulfide bond) form in the tertiary structure of a protein?

Answer 9

Two cysteine molecules in close proximity undergo an oxidation reaction to form cystine.

(Lose 2 protons and 2 electrons)

Question 10

What is the quaternary structure of a protein?

Answer 10

Multiple subunits bonded together.

Example: Hemoglobin, which is made up of 4 distinct subunits (a tetramer).

Question 11

What is a solvation layer (or solvation shell)?

Answer 11

A layer of water that surrounds a protein.

Solvation layer is what forces hydrophobic R groups to move towards the center of a protein.

Question 12

Which protein structure functions in cooperativity (or allosteric effects)?

Answer 12

Quaternary structure

One subunit can undergo a conformational change, which either enhances or reduces the activity of the other subunits.

Question 13

What are the five factors that stabilize the tertiary structure of a protein?

Answer 13

1. hydrophobic bonding
2. disulfide bridges
3. H bonds
4. van der Waals forces
5. ionic interactions

Question 14

What happens to a protein when it becomes denatured?

Answer 14

• it loses its tertiary (3d) structure
• becomes INACTIVE

Question 15

What is a protein’s conformation?

Answer 15

Its folded 3d structure and ACTIVE state.

Question 16

What are five agents that function in denaturing proteins?

Answer 16

1. heat
2. pH/salt (disrupt ionic interactions)
3. urea (disrupt H bonds)
4. enzymes
5. mercaptoethanol (disrupt disulfide bridges)