Week 1: Physical & Thermodynamic Foundations + Non-Covalent Interactions

dynamic steady state

• system remains stable & constant overall even if individual parts are constantly changing

• this is not equilibrium

• needs a constant input of energ

system

• everything within a defined region of space

• for chemical rxns in solution, system is all reactants, products & immediate atmosphere

• if havea DNA solution in a test tube, the DNA molecules itself would not be a system bc no defined boundaries

universe

system and surroundings

isolated system

no exchange of matter or energy w/its surroundings

closed system

exchanges energy but not matter matter w/its surroundings

open system

exchanges both energy and matter with its surroundings

• ex: living organisms

1st Law Thermo

energy isn’t created or destroyed, just converted

• ΔE = q + w

2nd Law Thermo

randomness in universe is always increasing

Entropy (S)

randomness or disorder of the components of a chemical system

• must be (+) for a rxn to be spontaneous

Free Energy (G)

amount of energy available to do work

• negative for a rxn that releases heat (exergonic)

• ΔG < 0 for process to be spontaneous

Enthalpy

• heat content, roughly reflecting number and kinds of chemical bonds & noncovalent interactions broken and formed

• ΔH = ΔE + PΔV

  • P = Pressure (constant) and V = Volume

• easily measured with a calorimeter, unlike Energy

Free Energy Equation

ΔG = ΔH_sys - TΔS_sys

ΔG for formation of proteins and nucleic acids is?

positive

• in living cells, these reactions can only occur because they are coupled with highly exergonic reactions (reactions with a negative such as the hydrolysis of ATP or GTP. The overall combined net ΔG < 0 for the coupled process

Oxidation of Glucose

C₆H₁₂O₆ + 6O₂ → 6CO₂ + 6H₂O

glucose + oxygen → carbon dioxide + water

• surroundings increase in entropy bc of releasing of heat and go from 7 molecules to 12 thay are more randomly distributed

Living organisms & entropy

we are highly ordered so entropy poor

the greater the elevation of a larger object, the ___ the energy (ΔG) released

greater

ΔG

defines energy change as system moves from its initial state to equilibrium, w/no changes in temp or pressure

Exergonic rxns

• products have less free energy than reactants bc rxn releases free energy, which is available to do work

ΔG°

• initial ΔG when you mix all reactants and product such that the concentrations are 1 M

• the change in free energy when it occurs under specific standard conditions

• changed depending on Temp

ΔG° equation

ΔG° = -RTlnK_eq at equilibirum

binding of enzyme to TS is ______

exergonic

Stoppered thermos ΔE

in a stoppered thermos of coffee (isolated system), heat can’t be given off bc of insulation and work can’t be done bc of rigidity so ΔE = q + w = 0 + 0 = 0

how does ΔH relate to ΔE

ΔH ≈ ΔE

• ΔH = ΔE + PΔV but unless a product produces or consumes a gas, ΔV is small so get ΔH ≈ ΔE

ΔS_total

ΔS_total = ΔS_system + ΔS_surroundings

DNA helix formation

• ΔS_sys < 0

  • 2 strands → 1 double helix

  • single strands more flexible

• ΔS_total> 0 & ΔS_surr > 0

  • forming bonds gives off heat to make ΔH_sys < 0

DNA annealing is ____ except at ____ temperatures

DNA annealing is spontaneous except at high temperatures

• at high temps, DNA spontaneously melts so ΔG<0

ΔS_surr

ΔS_surr = -ΔH_sys /T

if G>0, then process goes in _____

reverse direction

ex: DNA at high temp

Which interactions contribute favorable and unfavorably to DNA Double Helix Formation?

Favorably:

• H-Bonds

• VDW (largest contribution to -ΔH so major driving force for double helix formation

• pi-stacking (dipole-dipole interactionn between stacked bases)

Unfavorably:

• electrostatic interactions

Electrostatic Interactions DNA

• Phosphates have negative charges on DNA backbone so repulsions & coming together of like charges is unfavorable but since charges are on backbone, it’s not too bad

H-Bonds

• Hydrogen covalently bonded to Oxygen or Nitrogen bonded to an Oxygen or Nitrogen

• H₂O can form a max of 4 H-bonds (donate 2 and accept 2)

• H bonds in double helix stronger than H bonds single stranded DNA forms w/H₂O

• mix-matched bases are destabilizing but regular base pairing favors double helix formation

  
  

VDW Interxns

• weak attractions between neutral atoms

• individually weak in DNA, but base stacking makes them collectively strong

• base pairs are parallel and stacked near perfect fit

at equilibrium, ΔG = ?

ΔG = 0