Proteins and carbohydrates 2 Flashcards
What is ΔG from folded to unfolded state a measure of?
The thermodynamic stability of the protein.
Why does the observed ΔG from folded to unfolded state of a protein tend to be different from the theoretical value?
As there are so many interactions in a folded protein that small errors in predictions/calculations accumulate to relatively large differences.
What are the strongest bonds in proteins?
Covalent bonds
Why can electrostatic forces in proteins be strong?
Many atoms in proteins have partial charges which attract and repel; while the individual charges are small, the cumulative effect of those changes can be significant.
Why are proteins only marginally stable at in vivo temperatures?
Because for most proteins ΔG from folded to unfolded state is small (equivalent to a few non-covalent bonds).
What is the stability curve of a protein?
The plot of the free energy of protein unfolding as a function of temperature. The protein is stable at the temperature range at which ΔG from folded to unfolded state is ≥ 0.
What are some types of interactions between secondary protein structures?
Hydrogen bonds
Ionic bonds
Hydrophobic interactions
Disulphide bonds
What are important intra- and intermolecular interactions in proteins?
Ionic bridge
Hydrogen bonds
Electrostatic interactions
van der Waals interactions
Hydrophobic interactions
Name three types of protein denaturation (unfolding).
Thermal, mechanical, chemical (using chemical agents (e.g. urea)) denaturation.
How does urea promote protein denaturation?
Alteration of water structure:
- Reduction of hydrophobic effect
- Free water to compete with intraprotein interactions
Direct interaction of urea with polar residues and peptide backbone
- Stabilise non-native conformations
How does increasing denaturant concentration affect the thermodynamic stability curve of a protein?
The stability curve shifts downwards as denaturant concentration increases until the temperature window of protein stability (ΔG from folded to unfolded state is ≥ 0) vanishes.
What are thermophilic organisms?
Organisms that live in 55-80°C environments.
What are hyperthermophilic organisms?
Organisms that live in 80-113°C environments.
What are strategies for increasing protein stability?
- Broadening the free energy curve by reducing the change in heat capacity by having residual structure in the unfolded protein to decrease the change in heat capacity from folded to unfolded state.
- Reduced number of unstructured loop regions
- Increased amount of interactions between secondary structures
- Improved packing efficiency and reduced cavity sizes (more compact)
- Increased number of ion pairs and networks of ion pairs (thermophiles tend to have more charged amino acids than mesophiles)
- Reducing conformational entropy of the unfolded state of the protein
