Lecture 4

Question 1

Significance of free electrons vs lone pairs

Answer 1

free electrons - not bound to any specific atom
- essential for electrical and thermal conductivity

lone pairs - pair of valence electrons localized on a single atom, not involved in bonding
- influence molecular geometry
- nucleophiles
- enable intermolecular interactions like hydrogen bonding
- affect molecular polarity and dipole moments

Question 2

Difference between covalent and non-covalent interactions

Answer 2

covalent - stable
- formed by sharing of outer electrons, due to overlapping orbitals
- strongest bond
- peptide bonds, disulfide bonds
- phosphodiester bonds

non-covalent - greater distance than in covalent bonds
- hydrogen bonds interactions
- electrostatic interactions
- van der waals interaction
- hydrophobic effects

Question 3

Hydrogen bonds

Answer 3

• H bond forms between the hydrogen atom on the donor and the lone pair on the acceptor
• bond energy = 3-5 kcal/mol
• length = 3
• directional property - importance of orientation
• lone pairs on O and N act as H-bond acceptor
• sulfur on cysteine can act as a weak H-bond acceptor since it has lone pairs
• hydrogen bonding between bases in DNA, amide nitrogen hydrogen and carbonyl oxygen
• water molecules are cohesive, can H-bond to 4 other water molecules (1 for each hydrogen, 2 for each oxygen)

Question 4

Electrostatic interactions

Answer 4

• salt bridges
• bond energy = 4.8 kcal/mol
• charged amino acid side chains participate in electrostatic interactions to facilitate protein folding
• interaction between positive and negative charge

Question 5

Electrostatic interaction formula

Answer 5

E=K q1q2/Dr
- larger D = weaker interaction
- water has one of the highest D of any pure liquid

Question 6

Van der Waals (weak) forces - dipole interactions

Answer 6

• interactions occur between electrically neutral molecules
• polar molecules have permanent dipoles
• non-polar molecules can interact via these forces -> each atom has an electron cloud that fluctuates, yielding a transient electric dipole
• dipole of one atom can influence the electron distribution in another
• london dispersion forces = weakest
• repulsion occurs between atoms that are brought too close to each other

Question 7

Hydrophobic effect

Answer 7

• not a true force but a consequence of the energy need to insert a nonpolar molecule into water
• water naturally forms a hydrogen bond network, these must be broken to insert nonpolar molecules
• nonpolar form van der waal interaction among themselves and do not H-bond with water (difficult to solvate)
• organization required to dissolve nonpolar solutes (clathrates- form around nonpolar molecules)

Question 8

Entropy in hydrophobic effects

Answer 8

• arrangement of water molecules around each hydrophobic molecule is thermodynamically unfavorable
• organization of water molecules reduced when hydrophobic molecules associate with each other -> increasing entropy (disorder) of the system (thermodynamically favored)
• “attraction” between non-polar molecules in aqueous environment = hydrophobic effect
• default to lower energy state

Question 9

Protein folding and hydrophobic effect

Answer 9

• in an unfolded protein nonpolar or hydrophobic regions are exposed to water which organize itself around these regions
• in a folded protein hydrophobic regions often associate with each other and are shielded from the aqueous solvent
• less order is required for the water molecule to solubilize protein -> more favorable energetically

Question 10

Why is water an excellent solvent

Answer 10

• water is very polar
• forms hydration spheres around ions, proteins, and other molecules
• can solubilize polar compounds by forming H-bonds with these solutes
• ability of water to hydrate ions is great than tendency of opposite ions to attract one another