Lecture 2: Covalent and Noncovalent Interactions

importance of covalent interactions

hold together peptide chain

form peptide bonds

strength and weakness of non covalent interactions

individually weak but strong together

Types of non covalent interactions

Hydrogen bonding

hydrophobic effect

VDW

Electrostratic

what is the most important interactions in biochemistry

non- covalent

importance of non-covalent interactions

form greater order protein structures (secondary, tertiary, etc)

describe electrostatic interactions

charge/charge interactions

describe coloumbs law and its limiations

determines strength of electrostatic interactions

only takes into account charge not repulsize forces at close distances

where are electrostatic interactions found

nucleotide base interactions (COO- - - - NH3+

dialectric constant measures…

measure of a material’s ability to reduce the effective interaction between charged particles.

why do polar molecules have higher dialectric constants

• When an electric field is present (or when charged particles are nearby), the dipoles in a polar solvent can reorient themselves.

• This reorientation means that the positive ends of the dipoles are drawn toward negative charges, and the negative ends toward positive charges.

• This alignment of dipoles creates an opposing field that reduces the net electric field between the charges.

• As a result, the effective force (or Coulomb’s force) between two charged particles is diminished.

what type of interactions are VDW

diploe dipole

lennard jones PE graph accounts what what forces at what distances

• Attractive forces (e.g., dipole-dipole, van der Waals/London dispersion) at long range.

• Repulsive forces (due to electron cloud overlap) at very short distances.

Lowest PE peak on LJ graph

This lowest point (minimum of the curve) represents the most stable distance between the two atoms

At this distance, the attractive forces exactly balance the repulsive forces, meaning the system is at its lowest energy state (happiest).

past the lowest PE point

attraction weakens (energy approaches 0).

at E=0 describe the attraction and distance

• This point occurs when there is no net attraction or repulsion between two atoms.

• Physically, this represents when the atoms are far enough apart that they no longer interact significantly.

why are HB important to DNA and RNA

stabilize DNA/RNA structures (watson-crick base pairing")

stabilize protein structures (peptide bonds)

Hydrogen bonding is strongest in what conformation

linear

Define Hydrophobic effect

ability of water to aggregate/push together non polar molecules

Describe the Gibbs free energy that drives the hydrophobic effect

Initial interaction:

• delta S: entropy initially decreases as hydration shell that forms increases the ordering of the system

• delta H: minimally affected as water sacrifices HB to form shell (not favorable)

Result

• system aggregates non polar molecules

• minimizes their surface area

• minimizes amount of water molecules dedicated to hydration shell

• minimizes the initial ordering

• entropy of the system increases