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

What amino acid do disulphide bridges form between?

Answer 6

cysteine

Question 7

How do disulphide bridges form?

Answer 7

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

Question 8

What do non-covalent interactions dictate?

Answer 8

geometry and specificity

Question 9

Describe the structure of the leucine zipper

Answer 9

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

Question 10

In protein folding, what is ΔG equal to?

Answer 10

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

Question 11

What is the equation for ΔG in protein folding?

Answer 11

ΔG= ΔH-T ΔS

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

Question 12

How can water effect the energetics of protein folding?

Answer 12

• 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 13

Does breaking non-covalent interactions release energy?

Answer 13

no it requires energy

Question 14

In protein folding is ΔH usually +ve or -ve?

Answer 14

-ve