1.5 Tertiary and Quaternary Protein Structure [HY]

Question 1

Tertiary Structure

Answer 1

• A protein’s three-dimensional shape
• Tertiary structures are mostly determined by hydrophilic and hydrophobic interactions between R groups of amino acids

Question 2

Where are hydrophobic residues found?

Answer 2

• Interior of proteins

Question 3

Which bonds found in polypeptide chains form electrostatic interactions and hydrogen bonds?

Answer 3

• N-H (amino) and C=O (carbonyl)
• Stabilize the protein from the inside

Question 4

Where are hydrophilic residues found?

Answer 4

• On the surface of proteins
• Have polar or charged, R groups

Question 5

Another way 3-D structure can be determined?

Answer 5

• Hydrogen bonding.
• Acid–base interactions between amino acids with charged R groups, creating salt bridges

Question 6

Disulfide bonds

Answer 6

• the bonds that form when two cysteine molecules become oxidized to form cystine
• create loops in the protein chain

Question 7

Protein folding

Answer 7

• 1st secondary structures form first
• 2nd hydrophobic interactions and hydrogen bonds cause the protein to “collapse” into its proper three-dimensional structure
• extremely rapid process; less than a second

Question 8

Molten Globules

Answer 8

Protein folding intermediate state.

Question 9

Denaturation

Answer 9

• If a protein loses its tertiary structure
• sometimes reversible, often irreversible
• unfolded proteins cannot catalyze reactions

Question 10

Solvation layer

Answer 10

• Whenever a solute dissolves in a solvent, the nearby solvent molecules form this

Question 11

What happens when a hydrophobic side chain (like phenylalanine and leucine) is placed in aqueous solution?

Answer 11

• the water molecules in the solvation layer cannot form hydrogen bonds with the side chain. This forces the nearby water molecules to rearrange themselves into
  specific arrangements to maximize hydrogen bonding—which means a negative change in entropy
• A -delta S means larger delta G and lack of spontaneity

Question 12

What happens when a hydrophilic side chain (like serine or lysine ) is placed in aqueous solution?

Answer 12

• allows the nearby water molecules more latitude
  in their positioning
• increasing their entropy (ΔS > 0), and making the
  overall solvation process spontaneous

Question 13

Quaternary Structure

Answer 13

• not all proteins have quaternary structure
• Quaternary structures only exist for proteins that contain more than one polypeptide chain
• Made of small globular peptides, or subunits, and represents the functional form of the protein
  -Ex. hemoglobin and immunoglobulins

Question 14

Why do quaternary structures form?

Answer 14

• 1st: more stable, by reducing the surface area of the protein complex
• 2nd: they can reduce the amount of DNA needed to encode the protein complex
• 3rd: they can bring catalytic sites close together, allowing
  intermediates from one reaction to be directly shuttled to a second reaction
• 4th: can induce cooperativity, or allosteric effects (one subunit can undergo conformational or structural changes, which either enhance or reduce the
  activity of the other subunits)

Question 15

Conjugated Proteins

Answer 15

• derive part of their function from covalently attached prosthetic groups

Question 16

Prosthetic groups

Answer 16

• organic molecules, such as vitamins, or even metal ions, such as iron
• can also direct the protein to be delivered to a certain location, such as the cell membrane, nucleus, lysosome, or endoplasmic reticulum.

Question 17

Lipoproteins

Answer 17

• Proteins with lipid

Question 18

Glycoproteins

Answer 18

• Proteins with carbohydrate

Question 19

Nucleoproteins

Answer 19

• Proteins with nucleic acid prosthetic groups

Question 20

What is the prosthetic group of hemoglobin?

Answer 20

Heme, hemoglobin is inactive without the heme group