BIOC 307 Week 1 Learning Goals
Exam Study Guide
What is an ionic interaction (charge-charge interaction), and what other terms are used
to describe the same thing? - ANSWER Electrostatic attraction or repulsion between
charged groups. Another term to describe ionic interaction is "salt bridges/linkages,
electrostatic interactions"
How does the distance between two charged groups affect the energy of their
interaction? - ANSWER Inversely proportional. As R increases energy decreases
Coulomb's Law E=k(Q1Q2/Dr)
What are the relative values of the dielectric constants for a nonpolar solvent and a
polar solvent? - ANSWER Nonpolar solvent (hexane) ~2
polar solvent (H2O) ~80
How does solvent polarity affect strength of ionic interactions? - ANSWER As solvent
polarity increases, strength of ionic interactions decreases. Charge interactions in a
polar solvent (water) are relatively weak compared to those in a nonpolar solvent (the
interior of a protein) where the dielectric constant is low. Most charged groups stay on
the surface where they don't interact with other charged groups from the protein
because of high dielectric constant of water but are stabilized by hydrogen bonding and
polar interactions w/water.
What type of solvent is water? - ANSWER polar solvent
Is an ionic interaction stronger in a polar solvent or in a nonpolar solvent? - ANSWER
Nonpolar
What is a hydrogen bond? - ANSWER A hydrogen bond is a weak bond between two
molecules resulting from an electrostatic attraction between a proton in one molecule
and an electronegative atom in the other.
What is a hydrogen bond donor? - ANSWER An atom/molecule that supplies a free
hydrogen capable of making hydrogen bond
What is a hydrogen bond acceptor? - ANSWER An electronegative atom that can
hydrogen bond with the hydrogen bond donor (O, N, or F)
Distinguish "hydrogen bond donor/acceptor" from "proton donor/acceptor" (Bronsted
acid/base) - ANSWER Proton donor (Bronsted-Lowry acid): any species that is capable
of donating a proton (H+)
, Proton acceptor (Bronsted-Lowry base): any species that is capable of accepting a
proton, which requires a lone pair of electrons to bond to the proton (H+)
When an acid forms a conjugate base and a base forms a conjugate acid via the
exchange of a proton (Hydrogen atom being exchanged between the two)
In hydrogen bond donors and acceptors, a hydrogen atom itself isn't being exchanged
between molecules but is instead forming an intermolecular interaction.
Be able to identify chemical groups (and the specific atoms involved) that can serve as
hydrogen bond donors and groups which can serve as hydrogen bond acceptors. -
ANSWER Hydrogen bond donors: alcohols, water
Hydrogen bond acceptors: alcohols, water, carboxylic acid, amine, ketone
What are van der Waals interactions? - ANSWER Weak attractions between molecules
or parts of molecules that result from transient local partial charges.
How (qualitatively, not an equation) does the strength of Van Der Waals relate to the
distance between atoms? - ANSWER o Energy of a van der Waals interaction as any 2
atoms approach one another within about 4-5Å is related to the distance between them.
o Strength is strongest at 4-5 and decreases with increasing distance.
§ As atoms come closer, repulsive component of VDW forces predominates as electron
orbitals of adjacent atoms begin to overlap (Steric hindrance)
Why are such weak, nonspecific interactions important in biochemistry? (Van Der
Waals) - ANSWER o Individually very weak and nonspecific, but sum of many can be very
important in steric (shape) complementarity
§ Cause a polypeptide to fold
§ Thousands of van der Waals interactions involved in attaining native conformation.
What is the "hydrophobic effect"? - ANSWER o Hydrophobic effect: association of
nonpolar groups with each other in aqueous systems due to unfavorable interaction of
nonpolar groups/molecules w/water, resulting in a "preference" of hydrophobic groups
and molecules to minimize their exposure to water
o 2 nonpolar side chains come together → SA exposed to solvent ↓ → some highly
ordered water molecules in solvation shell are released to bulk solvent → entropy (ΔS)↑
→ thermodynamically favorable
o EX:
§ in transition from random to secondary conformation (𝛂-helix or 𝛃-structure, ~⅓ of
water of solvation about unfolded polypeptide lost to bulk solvent
§ Another ⅓ or original solvation shell lost when a polypeptide attains its native
Exam Study Guide
What is an ionic interaction (charge-charge interaction), and what other terms are used
to describe the same thing? - ANSWER Electrostatic attraction or repulsion between
charged groups. Another term to describe ionic interaction is "salt bridges/linkages,
electrostatic interactions"
How does the distance between two charged groups affect the energy of their
interaction? - ANSWER Inversely proportional. As R increases energy decreases
Coulomb's Law E=k(Q1Q2/Dr)
What are the relative values of the dielectric constants for a nonpolar solvent and a
polar solvent? - ANSWER Nonpolar solvent (hexane) ~2
polar solvent (H2O) ~80
How does solvent polarity affect strength of ionic interactions? - ANSWER As solvent
polarity increases, strength of ionic interactions decreases. Charge interactions in a
polar solvent (water) are relatively weak compared to those in a nonpolar solvent (the
interior of a protein) where the dielectric constant is low. Most charged groups stay on
the surface where they don't interact with other charged groups from the protein
because of high dielectric constant of water but are stabilized by hydrogen bonding and
polar interactions w/water.
What type of solvent is water? - ANSWER polar solvent
Is an ionic interaction stronger in a polar solvent or in a nonpolar solvent? - ANSWER
Nonpolar
What is a hydrogen bond? - ANSWER A hydrogen bond is a weak bond between two
molecules resulting from an electrostatic attraction between a proton in one molecule
and an electronegative atom in the other.
What is a hydrogen bond donor? - ANSWER An atom/molecule that supplies a free
hydrogen capable of making hydrogen bond
What is a hydrogen bond acceptor? - ANSWER An electronegative atom that can
hydrogen bond with the hydrogen bond donor (O, N, or F)
Distinguish "hydrogen bond donor/acceptor" from "proton donor/acceptor" (Bronsted
acid/base) - ANSWER Proton donor (Bronsted-Lowry acid): any species that is capable
of donating a proton (H+)
, Proton acceptor (Bronsted-Lowry base): any species that is capable of accepting a
proton, which requires a lone pair of electrons to bond to the proton (H+)
When an acid forms a conjugate base and a base forms a conjugate acid via the
exchange of a proton (Hydrogen atom being exchanged between the two)
In hydrogen bond donors and acceptors, a hydrogen atom itself isn't being exchanged
between molecules but is instead forming an intermolecular interaction.
Be able to identify chemical groups (and the specific atoms involved) that can serve as
hydrogen bond donors and groups which can serve as hydrogen bond acceptors. -
ANSWER Hydrogen bond donors: alcohols, water
Hydrogen bond acceptors: alcohols, water, carboxylic acid, amine, ketone
What are van der Waals interactions? - ANSWER Weak attractions between molecules
or parts of molecules that result from transient local partial charges.
How (qualitatively, not an equation) does the strength of Van Der Waals relate to the
distance between atoms? - ANSWER o Energy of a van der Waals interaction as any 2
atoms approach one another within about 4-5Å is related to the distance between them.
o Strength is strongest at 4-5 and decreases with increasing distance.
§ As atoms come closer, repulsive component of VDW forces predominates as electron
orbitals of adjacent atoms begin to overlap (Steric hindrance)
Why are such weak, nonspecific interactions important in biochemistry? (Van Der
Waals) - ANSWER o Individually very weak and nonspecific, but sum of many can be very
important in steric (shape) complementarity
§ Cause a polypeptide to fold
§ Thousands of van der Waals interactions involved in attaining native conformation.
What is the "hydrophobic effect"? - ANSWER o Hydrophobic effect: association of
nonpolar groups with each other in aqueous systems due to unfavorable interaction of
nonpolar groups/molecules w/water, resulting in a "preference" of hydrophobic groups
and molecules to minimize their exposure to water
o 2 nonpolar side chains come together → SA exposed to solvent ↓ → some highly
ordered water molecules in solvation shell are released to bulk solvent → entropy (ΔS)↑
→ thermodynamically favorable
o EX:
§ in transition from random to secondary conformation (𝛂-helix or 𝛃-structure, ~⅓ of
water of solvation about unfolded polypeptide lost to bulk solvent
§ Another ⅓ or original solvation shell lost when a polypeptide attains its native
