1

Example Problem

Calculate DGo for the reaction A + B C + D at 25 oC when the

equilibrium concentrations of [A] = 10 mM, [B] = 15 mM, [C] = 3

mM, [D] = 5 mM. Is the reaction exergonic or endergonic under

standard conditions?

• This is an equilibrium!!! Keq = [C][D]/[A][B]

• DGo = -RT ln Keq = -RT ln {[C][D]/[A][B]}

• Keq = {[3x10-6M][5x10-6M]/[10x10-6M][15x10-6M]}

• DGo = -(8.3145 J/K-mol)(298K) ln {0.1} = 5705 J/mol

• DGo = 5.7 kJ/mol

• Not spontaneous since free energy is positive (endergonic)

• Also makes sense because the concentrations of C and D are

less than A and B.

2

Chapter 2: Water

• Physical properties of water

– Structure of water

– Water as a solvent

– Hydrophobic effect

– Osmosis and diffusion

• Chemical properties of water

– Ionization of water

– Acid-base chemistry

– Buffers

3

Water is The Fundamental Chemical of Life

1. Nearly all biological molecules assume their

shapes (and functions) in response to the

physical and chemical properties of the

surrounding water molecules.

2. Most biochemical reactions happen in water.

3. Water is often directly involved in catalytic

reaction(s) supporting life. (H+, HO-)

4. The production of O2 from water and CO2 is a

fundamental process in plant biochemistry

(photosynthesis).

4

Structure of Water

+0.33e +0.33e

-0.66e

d+ d+

d-

5

Hydrogen Bonding in Water

ca. 1.8 Å

Sum of H (1.2 Å) and O (1.4 Å) VDW radii = 2.6Å

H-Bond Interaction Distance = 1.8Å

H-bond donor

H-bond acceptor

The oxygen atom in water has four sp3 hybrid orbitals

Two for the lone pairs and two for the hydrogens

+0.33e

d+

-0.66e

d-

6

ICE: Each water molecule has

four H-bonds – one for each of

the two hydrogen atoms

(donors) and two for each

oxygen (acceptor) atom.

Ice has lattice network of H-

bonds = Strong!

LIQUID: Water consists of

a rapidly changing 3D

arrangement of H-bonded

water molecules (3-4 H-bonds).

Density (water) = 1.0 g/ml

Density (ice) = 0.92 g/ml

Water expands on freezing

Ice Structure

7

8

• Dipole moments are

created by the

separation of (partial)

charges or by the

inducement of a

charge separation

• Recall that the

separation of charge

is due to differential

electronegativities of

atoms involved in

bonds

9

Molecules have a definite shape

C OB

A

O

H

HO

H

HO

H

OH

OHHH

OH

• A, B, C, and O all lie in

the same plane. This is

trigonal planar

• As the molecule becomes

larger the shape becomes

more complicated

• And may have many

different conformations

• Shape of molecules can

significantly depend on

water!

Chair Boat

Chair

10

Geometry and Polarity

d+ d-

• While C Cl is polar,

carbon tetrachloride is not.

The sum of the vectors

equals zero = nonpolar

molecule.

mCCl4: m1=m2=m3=m4

Therefore, m1+m2+m3+m4= 0

mCHCl3: m2=m3=m4 but not m1!

Therefore, m1+m2+m3+m4 is not 0!

C

Cl Cl

Cl Cl

m1

m2

m3

m4

C

Cl Cl

Cl

m2

m3

m4 H

CHCl3 is polar

11

• Dipolar nature of water

• Opposite orientation of waters around a cation vs. that around an anion.

Solvation of Cations (+) and Anions (-)

12

Water of Hydration

• Hydration - to be surrounded by H2O.

– A polar molecule is hydrated by the partial charge interaction of water molecules

– A non-polar molecule is hydrated by concentric “shells” of ordered shielding water molecules

– Multiple hydrogen-bonds increase solubility

• Hydrophilic molecules are those that “love” to be in water.

• Hydrophobic molecules are those that “hate” to be in water (remember – oil and water don’t mix).

13

• Water molecules

form hydrogen-

bonds with organic

functional groups.

• Note that water can

act as both a

hydrogen-bond

acceptor and donor

(simultaneously).

14

Hydrophobic Effect

• Hydrophobic effect: Water surrounds hydrophobic molecules to

maximize hydrogen bonding, minimizes hydrophobic contacts.

• Driving force is increased ordering of water molecules around the

hydrophobic molecule, entropically disfavored.

15

STRUCTURED WATER

A cage of water molecules surrounding a non-polar

molecule has more structure than the surrounding bulk

water.

DG = DH –TDS (+TDS = MORE ORDER!)

• Minimize the structuring of water,

• Hydrophobic molecules cluster together,

minimizing the surface area.

• Fewer water molecules are needed to organize

around a smaller surface area!!!

16

• Non-polar molecules

are hydrated in a

different way (i.e.

NOT via hydrogen-

bonds to the molecule

but rather by forming

cage-like structures)

• This results in the

“hydrophobic effect”

• Non-polar molecules

tend to congregate in

these water cages

17

Aggregation of Non-Polar Molecules in Water

Reduced Surface Area = Fewer Water

Molecules in Cage

18

Amphiphiles

• Many biological molecules contain both polar

and non-polar segments.

• Combined hydrophobic and hydrophilic

properties

19

Amphiphiles: Polar and Non-Polar

Detergents, Fatty acids, lipid molecules

• polar head; non-polar tail.

Proteins

• polar and hydrophobic regions; hydrophobic

interactions are the greatest contributor to the

three dimensional shapes of proteins.

Water is more concentrated than the molecules it

surrounds so the shear numbers of ordered molecules

is much greater. The greatest entropy is a function

of both the dissolved molecule and the solvent.

20

Amphiphiles form micelles, membrane

bilayers and vesicles To minimize the highly ordered “cage” of water, the

amphiphile is forced into a structure to maximize entropy.

DG = DH -TDS driven by TDS (minimize loss of entropy!)

Protein Structure: Amphiphiles and Hydrophobic

Effects

21

Ribbon Diagram of Triosephosphate Isomerase

Hydrophobic

Interior and

“Pockets”

Buried!

Hydrophilic

Surface

Residues

Exposed!

Protein Structure: Amphiphiles and Hydrophobic

Effects

22

Solvent Excluded Structure of Triosephosphate Isomerase

Hydrophobic

Interior and

“Pockets”

Buried!

Hydrophilic

Surface

Residues

Exposed!

23

Diffusion and Osmosis • Diffusion occurs by random movement of molecules into all

regions that are accessible to each molecule. This occurs

constantly and, at some point, there is an equal concentration of

molecules throughout all regions.

• Osmosis is the diffusion of solvent molecules (water) across a

barrier from regions of high concentration (pure water) to regions

of lower concentration (water containing dissolved molecules).

• Osmotic Pressure is the pressure necessary to stop osmosis of

solvent across a barrier. Proportional to solute concentration.

• Dialysis is a useful technique for separating small molecules

from large ones using the principle of osmosis through a semi-

permeable barrier. For example, ions and other small molecules

can be gradually removed from a solution of protein via

(repeated) dialysis.

24

Diffusion

• Diffusion results

from the movement

of molecules from

regions of high

concentration to low

concentration.

• Diffusion equalizes

the concentration of

molecules filling the

container.

25

Osmosis

• Osmosis results from

the movement of

molecules through a

semi-permiable

barrier.

• Osmosis occurs so as

to equalize the

concentration of

permeable species on

both sides of barrier

Water Solution Barrier Pure Water Water Concentration 1 < Water Concentration 2

26

• Small molecules diffuse across membrane-diluted into large

volume of solvent.

• Osmosis of solvent attempts to dilute the solution of larger

molecules in the dialysis membrane.

For Next Time:

27

Study Rest of Chapter 2 and Start Chapter 4.

Work through problems in Chapter 2 in

Textbook and Student Companion

Memorize the Amino Acids!!!

Labor Day, Monday Sept. 2, No Class!