Determinants of Protein Structure

Question 1

What is the 5th level of protein structure?

Answer 1

supramolecular (many protein subunits and complexes)

Question 2

What is the levinthal paradox and what does it assume?

Answer 2

the shape of a protein is specified by its amino acid sequence
-assumes that each amino acid backbone can be in 3 conformational states

Question 3

How must proteins fold?

Answer 3

in pre-arranged pathways and in a cooperative manner

Question 4

What restricts the number of protein shapes that can be made?

Answer 4

• chemical properties of atoms
• peptide bonds can only be formed in few orientations
• non-covalent bonds/interactions between amino acid side chains constrain the folding of a protein

Question 5

What are van Der Waals attractions?

Answer 5

small charge differences caused by electron cloud fluctuating causing attractions or repulsions

Question 6

How do disulphide bridges form?

Answer 6

when the sulfhydryl groups on cysteine are oxidised a disulphide bridge can form

Question 7

What do non-covalent interactions dictate?

Answer 7

geometry and specificity

Question 8

Describe the structure of the leucine zipper

Answer 8

The α-helices form a leucine residue at every second turn. These form a hydrophobic region running down one side of the helix

Question 9

In protein folding, what is ΔG equal to?

Answer 9

the energy released or (required) when a protein folds into a native conformation

Question 10

What is the equation for ΔG in protein folding?

Answer 10

ΔG= ΔH-T ΔS

ΔH= energy released due to non-covalent interactions
ΔS =change in molecular freedom
T= temp (K)

Question 11

How can water effect the energetics of protein folding?

Answer 11

• In an unfolded protein, water forms hydration sphere around hydrophobic amino acid side chains, as the water is ordered the entropy of the system is decreased
• Hydrophobic interactions between amino acid side chains release the water from the hydration spheres
• The water molecules therefore gain entropy as they are more disorganised so the entropy of the system (protein + solvent) increases

Question 12

What is the relationship between a proteins shape and its function?

Answer 12

The shape of a protein dictates the specificity and function of that protein

Question 13

What is the key driver of protein folding?

Answer 13

Hydrophobic associations dive protein folding and interactions between subunits

Question 14

How does the energetics of protein folding work?

Answer 14

Unfolded protiens have hydration spheres around hydrophobic amino acids.
Therefore since the water is ordered the entropy is decreased.

Upon folding, the hydration spheres disperse and the water gains entropy.

Question 15

What interactions are important for membrane protein structure and function?

Answer 15

Hydrophobic interactions