Molecules of life Flashcards
What is the gibbs free energy equation ?
∆G = H – T∆S
In a reaction:
Reactant –> Product
How would we work out the total ∆G ?
∆G = ∆G product - ∆Greactant
What does H stand for ? What does it depend on ?
Enthalpy
depends on Non-covalent interactions
What are some non-covalent interactions that can affect enthalpy ?
- Hydrogen bonding: base pairing, catalytic triad, weaker, anisotropic – based on the position of the lone pairs of electrons, there is an ideal orientation
- Electrostatic interactions (salt bridges): stronger, amines carbonyls, isotropic
- Van der vaals: weakest, transient asymmetry induces complementary asymmetry
What is pauli exclusion ?
to a certain point, the closer atoms get they repel – energetically unfavourable
rank hydrogen bonding, electrostatic interactions (salt bridges) and van der waals based on strength
electrostatic are the strongest, then hydrogen bonding then van der waals
What is S and what does it depend on ?
Entropy and depends on covalent structures and hydrophobic effects
what is meant by entropy depends on covalent structures
bonding and rigidity, more rigid = lower entropy
larger molecules have a greater entropy
functional groups can modify flexibility
What is the hydrophobic effect ?
hydrophobic residues isolate from the polar solvent, meaning the water can gain entropy and become more disordered allowing the protein to become more ordered resulting in an overall negative change in gibbs despite the protein becoming more ordered
How can we calculate entropy ?
S = KB log W KB = Boltzmann’s constant
How does resonance hybridisation affect entropy ?
restricts rotation so increases entropy, resonance gives double bond characteristics
What does more bond rotation lead to ?
lower entropincreasedincreased entropy
delocalized electrons can reduce … therefore … entropy
flexibility, lowers
Do folded proteins have a positive or negative gibbs ?
negative, more negative - more favourable
How does the enthalpy change during protein folding ?
stays the same as the bonds do change but the number of bonds stays constant, therefore the system remains balanced
How does the entropy of folding change ?
decreases
What is the significance of the KaiB protein ?
a cyanobacterial clock protein – 2 stable conformations very close in energy (isoenergetic)
- The minima of the energy diagram of the 2 states are similar unlike most proteins when one folded state is more negative than other conformations
- Changing the system can change the state
What does isoenergetic mean ?
2 stable conformations are similar energy leading to a double trough energy diagram
