Factors determining Sec and Tert

Question 1

What determines the 3D structure of a protein

Answer 1

The actual amino acid sequence

Question 2

What is denaturation

Answer 2

Loss of structure that can result in loss of function, doesn’t have to be complete unfolding

Question 3

Name the 5 conditions that can cause denaturation of proteins?

Answer 3

High temp, extreme pH, Organic solvents (Alcohol/Acetones), Solutes (Urea/Guanidine), Detergents

Question 4

Is denaturation reversible or nah?

Answer 4

Reversible if by heat or extreme pH

Question 5

What are the two models for protein folding

Answer 5

1. The obvious one, hierarchical so first alpha and beta then supersecondary etc
2. Initiated by spontaneous collapse of polypeptide into a compact site, mediated by hydrophobic interactions between nonpolar residues

Question 6

How does the protein fold into its unique tertiary structure?

Answer 6

Thermodynamically favourable.
Overall free energy change is negative.
-Conformational entropy
-Non-covalent interactions
-Hydrophobic effect
-Disulfide bonds

Question 7

What is conformational entropy?

Answer 7

Decrease of randomness and so decrease in entropy

Question 8

Why is having non covalent interactions favourable in the case of protein folding?

Answer 8

So that the protein can be folded without having to break any bonds, not too stable to break so there is the flexibility

Question 9

what is referred to as salt bridges

Answer 9

interactions between positively and negatively charged residues

Question 10

Why does extreme pH affect the salt bridges

Answer 10

At neutral pH, there are electrostatic attractive forces between oppositely charged residues but at extreme pH the bridge is broken

Question 11

which amino acids are good hydrogen donors/acceptors

Answer 11

Serine and Threonine

Question 12

Which amide protons and carbonyls in the polypeptide backbone can form hydrogen bonds with side chains?

Answer 12

The ones not involved in secondary structure

Question 13

What interaction can stabilise the tertiary structure of proteins?

Answer 13

Van der Waals interactions

Question 14

Amino acids with hydrophobic side chains in the polypeptide are buried where

Answer 14

within the core of the protein away from aqueous environment - stabilising the protein

Question 15

what is the hydrophobic effect?

Answer 15

Internalizing hydrophobic groups via folding increases the randomness of the surrounding water molecules and so yields an entropy increase. think about micelles and ting

Question 16

If the entropy is energetically unfavourable, what makes the overall free change negative

Answer 16

Large negative deltaH

Question 17

What is source of the large negative deltaH

Answer 17

energetically favourable interactions between groups within foldedmolecules
- noncovalent interactions such as Hydrogen, VdW, dipole

Question 18

Increase in entropy is due to what

Answer 18

hydrophobic effect

Question 19

summarise the 3 main things for stability of folded structure

Answer 19

unfavourable Conformational entropy, favourable enthalpy from intramolecular side group interactions, favourable entrpy change from hydrophobic groups

Question 20

why does thermal denaturation of protein occur over a narrow temp range?

Answer 20

Because proteins fold in a cooperative manner