JW - Protein Architecture

Question 1

What characterizes Amphipathic Helices in terms of hydrophilicity and hydrophobicity?

Answer 1

One side is hydrophilic, and the other is hydrophobic

E.g. caused by every 7th amino acid being hydrophobic

Question 2

How do Amphipathic Helices behave in water and lipid bilayers?

Answer 2

In water: Hydrophilic outside, hydrophobic inside

In lipid bilayer: Hydrophilic inside, hydrophobic outside.

Question 3

What is the key feature of Leucine Zippers in terms of amino acid composition?

Answer 3

Every 7 amino acids is a leucine, forming heptad repeats and dimers.

• Traditionally found as transcription factors

Question 4

How is protein tertiary structure stabilized, and what drives protein folding?

Answer 4

• Stabilized by multiple weak interactions.
• Folding is driven by the hydrophobic effect

Question 5

List three types of interactions that stabilize protein tertiary structure

Answer 5

• Van der Waals interactions
• Ionic interactions
• Hydrogen bonds

Question 6

What is present in the interior and exterior of the water soluble protein: Myoglobin?

Answer 6

Interior

• Many hydrophobic residues

Exterior

• Many hydrophylic residues

Question 7

What is the special property of Cysteine regarding protein structure?

Answer 7

Formation of disulfide bonds, contributing to protein stability

Question 8

Define quaternary structure and provide an example of a homo-dimer

Answer 8

Polypeptide chains assembling into multi-subunit structures

Example:

• DNA binding protein
• Cro of bacteriophage λ

Question 9

What are post-translational modifications?

Answer 9

Several different amino acid side chains can be covalently modified to alter protein function

Question 10

What are 4 features regarding post-translational modifications?

Answer 10

1. Typically reversible
2. Enzymatically catalysed
3. Enhance functional diversity
4. Local, temporal control of function

Question 11

What amino acids are commonly involved in phosphorylation?

Answer 11

Serine (Ser), Threonine (Thr), Tyrosine (Tyr) are commonly phosphorylated

Question 12

What mediates the catalysis of phosphorylation?

Answer 12

The reaction is naturally very slow.

Hence catalysed by kinases and removed by phosphatases

Question 13

What structural elements characterize the kinase domain? (3)

Answer 13

• N-lobe predominantly b-sheet
• ATP binding cleft
• C-lobe predominantly a-helix

Question 14

What states can a protein exist in?

Answer 14

Unfolded state
→ Native (Useful)
→ Disordered aggregate (Unfunctional)
→ Degraded aggregate (May form amyloid fibril) (Not good)

Question 15

What protein helps other proteins adopt their functions?

Answer 15

Chaperones

Question 16

How is it shown that 3D structure is encoded in the amino acid sequence?

Answer 16

1. Oxidation under denatured conditions leads to the formation of wrong disulfide bonds
2. However, renaturation first and then oxidation leads to correct disulfide bonds

=> Amino acid sequence on its own encodes the correct three-dimensional structure of a protein

Question 17

Describe the progression to the folded state in the Protein Folding Funnel.

Answer 17

Unfolded protein:

• many configurations
• many interactions between residues but few native-like interactions

Transition state:

• many contacts & key residues have native contacts (c.f. yellow spheres)

Native state:

• many interactions, all are native interactions

Native state must have many residue contacts with all of them translating to native interactions

Question 18

What infectious agent is entirely composed of the protein Prp, and what diseases does it cause?

Answer 18

Prion

Prion causes:

• BSE (mad cow’s disease)
• CJD in humans
• Scrapie in sheep

Question 19

What is the mechanism of Prp replication? (2)

Answer 19

Normal cellular Prpc spontaneously converts to PrpSc

PrpSc catalyses the accumulation of more misfolded proteins from normal proteins

Question 20

Differences: Prpc and PrPSc

Answer 20

PrPSc: richer in β-strand

Question 21

What common feature is associated with protein misfolding in diseases?

Answer 21

Formation of amyloid deposits

• Often characterized by common β-structure in misfolded fibers (amyloid)