Factors determining Sec and Tert Flashcards
What determines the 3D structure of a protein
The actual amino acid sequence
What is denaturation
Loss of structure that can result in loss of function, doesn’t have to be complete unfolding
Name the 5 conditions that can cause denaturation of proteins?
High temp, extreme pH, Organic solvents (Alcohol/Acetones), Solutes (Urea/Guanidine), Detergents
Is denaturation reversible or nah?
Reversible if by heat or extreme pH
What are the two models for protein folding
- The obvious one, hierarchical so first alpha and beta then supersecondary etc
- Initiated by spontaneous collapse of polypeptide into a compact site, mediated by hydrophobic interactions between nonpolar residues
How does the protein fold into its unique tertiary structure?
Thermodynamically favourable. Overall free energy change is negative. -Conformational entropy -Non-covalent interactions -Hydrophobic effect -Disulfide bonds
What is conformational entropy?
Decrease of randomness and so decrease in entropy
Why is having non covalent interactions favourable in the case of protein folding?
So that the protein can be folded without having to break any bonds, not too stable to break so there is the flexibility
what is referred to as salt bridges
interactions between positively and negatively charged residues
Why does extreme pH affect the salt bridges
At neutral pH, there are electrostatic attractive forces between oppositely charged residues but at extreme pH the bridge is broken
which amino acids are good hydrogen donors/acceptors
Serine and Threonine
Which amide protons and carbonyls in the polypeptide backbone can form hydrogen bonds with side chains?
The ones not involved in secondary structure
What interaction can stabilise the tertiary structure of proteins?
Van der Waals interactions
Amino acids with hydrophobic side chains in the polypeptide are buried where
within the core of the protein away from aqueous environment - stabilising the protein
what is the hydrophobic effect?
Internalizing hydrophobic groups via folding increases the randomness of the surrounding water molecules and so yields an entropy increase. think about micelles and ting
If the entropy is energetically unfavourable, what makes the overall free change negative
Large negative deltaH
What is source of the large negative deltaH
energetically favourable interactions between groups within foldedmolecules
- noncovalent interactions such as Hydrogen, VdW, dipole
Increase in entropy is due to what
hydrophobic effect
summarise the 3 main things for stability of folded structure
unfavourable Conformational entropy, favourable enthalpy from intramolecular side group interactions, favourable entrpy change from hydrophobic groups
why does thermal denaturation of protein occur over a narrow temp range?
Because proteins fold in a cooperative manner
