Water, thermodynamic|Graduate Biochemistry 1| Tulane

Co-Author: Haoyang liang

Structure of Water

What makes water unique

1. Dipole

   • oxygen is tetrahedral (sp³ hybridization)

   • 4 orbitals

   • 4 pairs of electrons

     • 2 of them bind to protons
     • 2 of them are just orbitals

   • orbital is not completely random

     • Electrons spend more time around positively charged protons.
     • which cause the water dipole

   • In a right distance and right angle, they’ll form a hydrogen bond

   • In the water, there are lots of polar, dipole interactions which not form hydrogen bonds.

   • Hydrogen bond was much dominant in the water interaction with other biomolecules.

2. Small Size

   • small size and so, you have extrema abundant of a polar group.

Hydrogen bond

How it formed:

• Require hydrogen donor (δ+) and hydrogen acceptor (δ-) groups
• A hydrogen acceptor has a free electron pair
• Hydrogen is shared between the groups
• Separation and geometry are conserved
  Common Atoms you know
• Oxygen has 2 bonds and 2 free electron pairs (only accept)
• Nitrogen often has three bonds and 1 free electron pair and sometimes 4 bonds and no free electron pairs (accept other protons)
• Carbon has four bonds and NO free electron pairs and does not form hydrogen bonds

Double bonds make the atoms in a co-plane.

Other things about water

The number of hydrogen bonds

• Liquid water: ~3 hydrogen bonds/molecule.
• Ice: 4 Hydrogen bonds/molecule.

Quantity:

• The molar concentration of water is ~55M.
• The concentration of Hydrogen bonding groups in water is 220 M.
  • Which makes water is extremely polar
  • This character drives the most unique properties of the water

Common Chmeical Group

• Remember them all in slides - -
• Thinking about hydrogen bonding.

DNA pairs

© ATbio

Ionic Interaction

© wps.prenhall.com

All polar molecular has dipoles. This property makes them can interact with a hydrogen bond.
The water automatically circles the dipole molecules by ion interaction.

• charge-charge (can over distance)
• Dipole-dipole (weak than c-c)
• charge-dipole interactions
  • Exp: water circle the charged particles to form a water shield.
  • it limited the charge-charge interaction
    At the surface of the protein, not surrounded by water, the interaction of molecules here could become much stronger. (Con contain? ion, not shield by water)

• Dielectric constant of the medium (weaker in more polar solvents)
• Ionic strength of the solution (weaker as ion concentration increases)

Hydrophobic Interaction

The measure of the non-favorite interaction of nonpolar molecules

A non-polar molecule or group is “Hydrophobic”
doesn’t solve into water

Being nonpolar, not really interact with water.

• surface tension
• water molecules can’t H bond with nonpolar solutes so they H-bond with each other, forming a “cage”
• this ordering (entropy) is unfavorable
• the hydrophobic effect is proportional to the nonpolar surface area that is exposed to water

Exp:

1. a bottle of water, take non-polar (CH₄) into the water, happens nonthing
2. remove water-water interaction: lost some classic phenomenal

summary of interaction energies

• Covalent
• Ionic
• Hydrophobic
  • Thermol dynamic favorable.
• Hydrogen Bond
• Dipole-Dipole
• Induced dipole (Van Der Waals)

Ionization of Water

$H_ 2O \longleftrightarrow H^ + + HO ^ -$

$$
k = {\frac{[H^ +][OH^ -]}{[H_2 O]} } = 1.82 \times 10^ {-16}\ Molar
$$

Since H2O is constant (55.3 M), we can write
$$
K^ * = k[H_2 O] = [H^ +][OH^ -] = 1.01 \times 10^{-14}
$$
which usually rounded into 10^-14
$$
pH = -log([H+])
$$

Ionization Equilibria

low Ph -> proton concentration is high in water
high Ph -> low proton concentration

$$
pK_ A = -log(K_ A) = -log(\frac{[H^ +][A]}{[AH]})
$$

$$
pK_ A = -log([H^ +])-log(\frac{[A]}{[AH]})
$$

Henderson-Hasselbach Equation
$$
pK_ A = pH - log(\frac{[A]}{[AH]})
$$

Middle of the curve is pK_a: point tow portion equally abounded

Thermodynamic and Energetics

• Spontaneity of chemical reactions
• Chemical Potential, Equilibrium, standard states
• Equilibrium constants & Free Energy
• Coupled reactions
• High energy compounds
• Metabolic pathways - glycolysis

Second Law of Thermodynamic
In biology, we focus in:

• constant pressure, constant temperature

$\Delta H - T \Delta S < 0 $ is the energy we can use

$- \Delta G$ is spontaneous, is a thermodynamically favorable reaction

$aA + bB \longleftrightarrow cC + dD$

$$
\Delta G = \Delta G^ {\circ} + RT\ ln[\frac{C^ c D^ d}{A^a B^b}]
$$

The rate of a chemical reaction is INDEPENDENT of $\Delta G,\ \Delta G^ {\circ}$

$$
\Delta G ^ {\circ} = - RT\ ln[K_ {eq}]
$$

• Enzymes CAN NOT change the equilibrium concentrations in a reaction
• Enzymes can ONLY allow reaction to proceed towards equilibrium

Metabolic pathways

• often operate far from equilibrium
• are steady state pathways
• are irreversible because at least one step has large negative $\Delta G ^ {\circ}$

• The forward pathway is highly favorable (the sum of all the ΔGo is negative)
• Flow through the pathways is from A to J (the sum of all the ΔG is negative)
• Reactions 2,6,7 and 8 are near equilibrium
• Reaction 4 (D→E) is highly unfavorable
• Reactions 1,3, 6 and 9 are highly favorable
• Reactions 1,3 and 9 are far from equilibrium