Protein Folding Flashcards
Remember peptides are written from N-terminusto C-terminus by convention.
No - they are chiral.
What are the types of protein folding? [5]
- Folding
- Denaturing
- Unfolding
- Misfolding
- Aggregation
Describe the flow of information in cells.
- ATG - start codon
- TAA - stop codon (one of the 3 stop codons)
What is the genetic code?
- Some redundancy
- Implication is that silent mutations can occur
Proteins are synthesized during […]
translation
Describe the speed of protein folding.
Proteins fold quickly.
What is Levinthal’s Paradox (1968)?
- Proteins do NOT sample all conformations
- Folding is not entirely a random search
What is Anfinsen’s Hypothesis (1970s)?
- Native state = most thermodynamically stable state under specific solution conditions like temperature, pH, etc…
- Amino acid sequence encodes folded structure
How has a protein evolved to fold?
- Sequence determines folded structure
- So if you put a protein in water, hydrophilic (polar/charged) amino acids will form the surface and the hydrophobic interactions will form the interior of the molecule
- Major driving force of the collapse of the linear polypeptide chain is the hydrophobic effect.
- Like an emulsified oil droplet in water.
- Major driving force of the collapse of the linear polypeptide chain is the hydrophobic effect.
What is the hydrophobic effect?
- Water molecules maximize hydrogen bonds to lower entropy
What is protein folding a competition between?
- Enthalpic vs entropic effect
- Increase in entropy is favoured (entropy of water is increased as protein folds; hydrophobic effect favours protein folding)
- Decrease in enthalpy is favoured
- Protein is rigid - less entropy; conformational energy penalty
- As bonds are formed; heat is released
Proteins are only […]
marginally thermodynamically stable
What are the delta-G values for specific proteins?
About as strong as an H-bond!
Proteins are sensitive to their environment.
What is the effect of temperature?
Affects molecular dynamics (mainly entropic)
Proteins are sensitive to their environment.
What is the effect of pH?
Affects electrostatic interactions of protein; surface charges; protein hydration
Proteins are sensitive to their environment.
What is the effect of salt?
Affects electrostatic interactions of protein; surface charges; protein hydration
Proteins are sensitive to their environment.
What is the effect of pressure?
- Folded proteins exclude water from inner core
- Pressure favours state with lowest excluded volume
i.e., excluded from the solvent (therefore you can unfold the protein if you increase the pressure high enough)
Proteins are senstive to their environment.
What is the effect of force?
e.g., shaking; blending; extrusion
- Incorporation of air bubbles
- Air is more hydrophobic than water
- Proteins adsorb to air-liquid interface and denature, exposing their hydrophobic groups to the air
This could be done with oil instead of air as well.
e.g., whipping egg whites denatures the proteins and causes foam formation
Air is more hydrophobic than water.
True or False?
True.
Water is more hydrophobic than air.
True or False?
False.
Air is more hydrophobic than water.
Proteins are sensitive to temperature - what causes this increase in heat capacity?
Due to the structuring of water around the exposed hydrophobic side chains
Hydrophobic effect tapers off; conformational entropy dominates = unfold!
Proteins are sensitive to temperature. Describe how different proteins have different sensitivities to temperature.
- The peak is the maximum thermal stability
- ΔG values are hard to predict; so these values are determined experimentally
Note the cold denaturation that can occur.
Proteins are sensitive to salt - what are the effects of these various sodium salts on the temperature of denaturation of beta-lactoglobulin at pH 7.0?
- Stabilizing: screening of repulsive interactions (e.g., two negative charges near one another)
- Destabilizing: dehydration of protein/reduce hydrophobic effect
Proteins are sensitive to pH.
Use pepsin as an example and describe how.
No bulk water = […]
Limited dynamics
Water content influences […]
stability
Inversely stated: protein concentration influences stability.
Describe the effect of water content on the stability of ovalbumin.
smaller ΔH, presumably even smaller ΔSconf!
* At low water content (high protein concentration) - stability is very high
No bulk water = limited dynamics
Describe protein folding in a dilute solution versus a crowded solution.
- ΔHbond = smaller more unfolded state interactions
- ΔShyd = smaller lower entropy overall (less bulk water)
- ΔSconf = smaller unfolded state is > restricted
What are structural transitions in food processing? [5]
- Denaturation
- Unfolding
- Aggregation
- Precipitation
- Gellation
Important to understand how environment affects protein stability and structure (e.g., UV light; radiation; inhibitors; ligands; small molecules (e.g., sugars; phenolic compounds); temperature; pH; salt; pressure; force)
Structual transitions in food processing are […] to certain applications.
Detrimental
e.g., protein beverages where denaturation may lead to flocculation, precipitation
Structural transitions are […] to the functionality of many proteins.
essential
e.g., improve ability to stabilize foams, gel, emulsions; improve digestibility
What is precipitation?
Protein becomes insoluble
* may/may not follow denaturation, unfolding, aggregation
* change in solution conditions (pH, salt, temperature)
* precipitation at pH ~ pI (net charge is zero)
What is aggregation?
Formation of protein oligomers
* Change in quaternary structure
* Change in secondary, tertiary structure
* Can be amorphous or highly ordered
What is gelation?
Formation of network that traps solution
* Follows denaturation, unfolding and/or. aggregation
* Proteins remain soluble (initially)
* Inter-strand bonding (covalent; ionic; polar; non-polar)
What is collagen?
- Major component of bone, teeth, tendons, ligaments, skin & blood vessels
What do all gels share?
Formation of a network
What is foaming?
Foams are two-phase material systems where a gas is dispersed in a second, non-gaseous material, specifically, in which gas cells are enclosed by a distinct liquid or solid material.
Extensive aggregation = foam breakdown!
