Players and Forces

2017-09-27


Conceptual goals

  • Know the main chemical forces that undergird life
  • Understand the basis of the hydrophobic effect
  • Know how the four main classes of biomolecules differ in these properties.

Skill goals

  • Reason about the relative importance of different molecular forces in an aqueous environment
  • Identify the ability to participate in different interactions from structure.

If $\Delta G < 0$ for $A \rightleftarrows B$, the reaction favors:

  1. $A$
  2. $B$
  3. Neither
  4. It depends

$B$

At equilibrium, $[A] > [B]$ for $A \rightleftarrows B$. This implies:

  1. $\Delta G ^{\circ}> 0$
  2. $\Delta G ^{\circ}< 0$
  3. Neither

$\Delta G > 0$

Explain what this equation means:

$\Delta G = \Delta H - T \Delta S$

Where a reaction ends up ($\Delta G$) depends on:

  • Changes in the bonds formed (enthalpy, $\Delta H$)
  • Change in the disorder (entropy, $T\Delta S$)

Road map

What are the important molecular interactions?

What about water?

Biological molecules and these interactions

What is the ratio of formed to unformed for covalent bonds at equlibrium?

$A + B \rightleftharpoons AB$

$K = \frac{[AB]}{[A][B]}$

Useful info: $R = 0.0083\ kJ \cdot mol^{-1} K^{-1}$, $T = 300\ K$

Ratio of formed to unformed is given by:

$\Delta G = -RTln(K)$

$K = \frac{[AB]}{[A][B]} = e^{--\Delta G/RT}$

$K = e^{--400/(300*0.0083)} = 6 \times 10^{69}$

Question:

The energy of a $Na^{+}$ + $Cl^{-1}$ bond in vacuum is $\approx -400\ kJ\cdot mol^{-1}$, but the book says ionic interactions are $\approx -70 kJ \cdot mol^{-1}$ in proteins. What is the origin of this difference?

Protip: water is 55 M and should never be ignored

Question:

The energy of a $Na^{+}$ + $Cl^{-1}$ bond in vacuum is $\approx -400\ kJ\cdot mol^{-1}$, but the book says ionic interactions are $\approx -70 kJ \cdot mol^{-1}$ in proteins. What is the origin of this difference?

Water competes the partners in an ion pair, this (effectively) weakens the bond.

Key point: The strength of an interaction depends on its context!

What happens if you jam a random molecule into water

Disrupts smooth handoff of one water to another

Solutes throw off a water molecule's "groove".

Fewer degrees of freedom means drop in entropy.

Drop in entropy makes the dissolving the compound less favorable.

$$\Delta G = \Delta H - T \color{red}{\Delta S}$$

Uber nerds:

$V_{old} = \frac{4}{3} \pi r_{old}^{3} $
After merging, you have a sphere of $2 \times V_{old}$ with a radius:
$(2 \times V_{old}) = \frac{4}{3} \pi r_{new}^{3} $
$(2 \times \frac{4}{3} \pi r_{old}^3) = \frac{4}{3} \pi r_{new}^{3} $
$(2 \times r_{old}^3) = r_{new}^{3} $
$r_{new} = 2^{1/3} \times r_{old}$
Now compare surface areas:
$2 \times 4 \pi r_{old}^2 \stackrel{?}{>} 4 \pi r_{new}^{2}$
$2 \times r_{old}^2 \stackrel{?}{>} (2^{1/3} r_{old})^{2}$
$2 > {2}^{2/3}$

What happens when you create a molecule with both hydrophobic and polar character?


wikimedia

How hydrophobic is the molecule?

What interactions can it make?

What sorts of biological functions might it fulfill?

A

B

C

D

A


sugars

B


nucleic acids

C


amino acids

D


lipids

Summary

  • Biomolecules are built (mostly) from CHNOPS
  • These atoms participate in covalent, ionic, hydrogen-bond, and van der Waals interactions
  • Water can change the net strength of these interactions
  • The "hydrophobic effect" works to minimize the amount of solute surface interacting with water
  • Most biomolecules are "amphipathic," leading to self-organization
  • The four main molecular building blocks (sugars, nucleic acids, amino acids, and lipids) differ in these properties allowing them to fulfill different roles