Lec2 - Non-Covalent Bonding Flashcards
What two groups are common hydrogen donors (in H bonding)?
Amino group and Hydroxyl Group
Which are the strongest and weakest types of non-covalent bonding discussed?
Strongest: charge-charge interactions
Weakest: Van der Waals forces
Between: H bonds (and the hydrophobic effect?)
Why does the position of the ions within a protein affect the strength of charge-charge interactions (and where will it be stronger/weaker)?
Weaker on the surface: screening by counter-ions and by water itself
Stronger and stable when buried within the hydrophobic interior of the protein as less screening
Describe the arrangement of atoms in which H bonds exist
When a H atom is “sandwiched” between 2 hydrogen donors (N or O), and all three atoms are aligned
Which atom in a hydrogen bond is the hydrogen donor, and which is the acceptor?
The one covalently bonded to H is the donor, the one no covalently bonded is the acceptor
Which three groups are common hydrogen acceptors?
-N= ; -O- ; -CO-
Which type of non-covalent interaction is stronger than H bonds?
Electrostatic (charge-charge) interactions between opposite charges
Apart from strength, in what other sense are electrostatic interactions “superior” to H bonds?
They extend over greater distances
Are charge-charge interactions stronger on the surface of proteins, or near the centre?
Near the centre:
At the surface there can be shielding/screening by counter-ions, or by water itself; ions buried within the hydrophobic interior are more stable as less screening, so stronger
What effect does distance have on the strength of Van der Waals forces?
Molecules must be very close together for VDW forces to have any real effect; however, if they are TOO close together, the repulsive charges of their electrons will outweigh the attractive VDW forces
Van der Waals forces occur between what?
Between any two permanent OR inducibile dipoles
Why do inducible dipoles occur?
Due to random electron asymmetry within non-polar molecules
Why do Van der Waals forces matter if they are so weak?
In large molecules (e.g., DNA), there can be a great number of them, which helps to stabilise the molecule
Describe how the hydrophobic effect results in particular arrangements
Hydrophobic molecules force water molecules into specific, ordered arrangements (not entropically favourable); by clustering hydrophobic molecules together, fewer water molecules are trapped in ordered arrangements, making such an arrangement more entropically favourable
(Note: NOT based on ordered arrangements)
