Chapter 4: Protein Structure, Folding, and Function

Question 1

Name the acidic amino acids

Answer 1

Aspartate and Glutamate

Question 2

Name the basic amino acids

Answer 2

Histidine, Lysine, Arginine

Question 3

Which amino acids are most likely to phosphorylated and why?

Answer 3

Threonine, Tyrosine, Serine

–Because they have an exposed hydroxyl (OH) group

Question 4

What is the average molecular weight?

Answer 4

110 daltons

Question 5

Which amino acid participates in di-sulfide bonds?

Answer 5

Cysteine

Question 6

Which amino acid’s R-group disrupts the formation of an alpha-helix?

Answer 6

Proline

Question 7

How are beta-pleated sheet and alpha helices formed?

Answer 7

By the formation of hydrogen bonds between the backbone atoms of the polypeptide. Some are conducive to helix formation, while others are not

Question 8

How is tertiary structure formed?

Answer 8

By interactions between side-chain (R-group) atoms. Also, hydrogen bonding of hydrophilic side-chains with water in the protein’s environment also influences tertiary formation.

Question 9

What are the four types of bonds found in tertiary and quaternary structure formation?

Answer 9

• 1—Di-sulfide bonds (a type of covalent bod) create strong links between certain areas of the same polypeptide
• 2—van der Waals Interactions
• 3—Ionic Bonds
• 4—Hydrogen Bonds

Question 10

Describe Ion Exchange Chromatography

Answer 10

i. Proteins are sorted by charge
ii. The gel contains cations or anion groups. The proteins are eluted (removed by washing with a solvent) from the column with an increasing gradient of salt solution
iii. Their release depends upon the nature of the charged amino acid residues

Question 11

Describe Gel-Exclusion Chromatography

Answer 11

i. Proteins are sorted by size
ii. Resin is composed of hollow beads with pores of a particular size; large proteins move around the beads and so elute earlier than smaller proteins that can enter the resin pores and thus take a longer path through the column

Question 12

Describe Affinity Chromatography

Answer 12

i. Proteins are sorted by the type of ligand they bind.
ii. A selected ligand is covalently coupled to the column resin, and the protein mixture is applied. Elution can be performed with a salt solution but is often done with a solution of the ligand itself, which binds to the active site of the protein, releasing it from the resin-bound ligand. Because ligand binding can be very specific to a protein, this technique is often highly selective for the protein of interest

Question 13

What is electrophoresis?

Answer 13

The movement of charged particles in a fluid or gel under the influence of an electric field

Question 14

What does assay mean?

Answer 14

Qualitatively assessing or quantitatively measuring the presence or amount or the functional activity of a target entity (the analyte).