Topic 2: Protein Structure & Folding

Question 1

What are the chemical properties of amino acid residues?

Answer 1

• Hydrophilic / hydrophobic
• Polar / non-polar
• Acidic / basic

Question 2

What are the physical properties of amino acid residues?

Answer 2

Aliphatic or aromatic

Question 3

Why are some amino acid residues charged?

Answer 3

The ionization states of amino acids when put into water would depend on its pKa. If the amino acids’ pKa is less than the pH of the solution, it will be deprotonated. If the amino acids’ pKa is more than the pH of the solution, it will be protonated.

Question 4

What is the structure of an amino acid?

Answer 4

A central carbon atom covalently bonded to:

• an amino group
• a carboxyl group
• a hydrogen atom
• a R group

Question 5

What is the structure of a peptide bond?

Answer 5

Linking of two amino acids is accompanied by the abstraction of a molecule of water

Question 6

What are the properties of a peptide bond?

Answer 6

• Planar
• Rigid
• Always adopt a trans conformation
• Bonds on either side of the peptide bond are free to rotate

Question 7

What is the primary structure of proteins?

Answer 7

Linear amino acid sequence of the polypeptide chain

Question 8

What is the secondary structure of proteins?

Answer 8

Local spatial arrangement of polypeptide backbone

Question 9

What are the key features and properties of the alpha helix?

Answer 9

• H bonds between N-H and C=O stabilize the structure of the alpha helix
• 3.6 aa / turn
• 0.54nm pitch
• Right handed-helix

Question 10

What are the key features and properties of the beta sheet?

Answer 10

• Composed of beta-strands
• Stabilized by H-binds
• Distance between adjacent amino acids ~0.35nm

Question 11

What is a tertiary structure?

Answer 11

Overall 3D configuration of the protein

Question 12

What are globular proteins?

Answer 12

• Compact structure

- Usually several types of secondary structures

Question 13

What are fibrous proteins?

Answer 13

• Extended conformation

- Single type of repeating secondary structure

Question 14

What is the quaternary structure of proteins?

Answer 14

Association between different polypeptides to form a multi-subunit protein

Question 15

What are the types of bonds involved in maintaining the primary protein structure?

Answer 15

Peptide bonds

Question 16

What are the types of bonds involved in maintaining the secondary protein structure?

Answer 16

Hydrogen bonds

Question 17

What are the types of bonds involved in maintaining the tertiary protein structure?

Answer 17

• Hydrophobic interactions between R groups (hydrophobic R groups will seek to avoid water and position themselves in the center of the protein)
• Hydrogen bonding in polypeptide chains and between amino acid R groups
• Ionic bonding between positively and negatively charged R groups that come close to each other
• Covalent bonding between R groups of cysteine amino acids (disulfide bridge)
• Van der Waals’ forces between molecules

Question 18

What are the types of bonds involved in maintaining the quaternary protein structure?

Answer 18

• Intermolecular forces

- Disulfide bonds can also be found

Question 19

How do proteins fold?

Answer 19

• Ordered process
• Localized folding and with stable confirmations maintained
• Driven by the need to find the most stable conformation

Question 20

Why is protein folding important?

Answer 20

Protein misfolding can cause disease

Question 21

Why does protein misfolding cause disease?

Answer 21

• Loss of function: proteins don’t work the way they were supposed to
• Misfolded proteins can be converted into shapes that are unfavorable to the crowded cellular environment (hydrophobic on the outside instead of inside)