Chemistry 114A - : Biochemical Structure and Function

Chemistry 114A –
Biochemical Structure
and Function
Chapter 2: Water
Water is an Essential Component of Life
Organisms on planet earth are mostly water (humans ~70%)

Biology/Biochemistry is best understood in the context of the aqueous
environment
Water is central to biochemistry for the following reasons:

1. Water determines the shapes of macromolecules
2. Most biochemical reactions occur in water (few exceptions)
3. Water actively participates in most biochemical reactions
Structure of Water (Dihydrogen Monoxide)
H2 O
HOH
H-O-H
Why is water is not arranged linearly?

Water Deviates from Traditional Tetrahedral Geometry
Water has four sp3

hybrid orbitals
Hydrogen Bonding
Donor group
Weakly acidic
Acceptor group
Weakly basic
How many H-bonding

pairs possible?
Hydrogen Bonding
Donor group
Weakly acidic
Acceptor group
Weakly basic
How many H-bonding

pairs possible?
Hydrogen Bonding Strength Depends on Geometry
~5-20 kJ mol-1
The Irregular Structure of Water - Fluidity
• Each molecule of liquid water reorients about once

every 10-12 s
• Each molecule is h-bonded to ~3.4 nearest neighbors
• H-bonds are distorted, irregular and varied
• Forms clusters of 3 to 7-membered rings
• Liquid water = rapidly fluctuating clusters

Crystallization of Water – Ice Formation
• Freezing of water – 6 regular H-bonding

partners
• Water expands upon freezing
• Density decreases (1g/mL -> 0.92 g/mL)
Is the freezing of water

entropically favored?
Bond Energies in Nature
Coulomb’s Law
Proportionality constant
Energy Charge 1, Charge 2
Dielectric Constant Distance
1 3 ~78
Dielectric Constant
Nonpolar
Vacuum Solvent Water
What happens when you move two charges

from water to nonpolar solvents?
CHECKPOINT
• Sketch a diagram of a water molecule and indicate the ends that

bear partial positive and negative charges.
• Compare the structures of ice and water with respect to the

number and geometry of hydrogen bonds.
• Which of the functional groups listed in Table 1-2 can function as

hydrogen bond donors? As hydrogen bond acceptors?
• Describe the nature and relative strength of covalent bonds, ionic

interactions, and van der Waals interactions (hydrogen bonds,
dipole–dipole interactions, and London dispersion forces).
The Dipolar Nature of Water
partial negative charge (δ−)

of −0.66e,
partial positive charge (δ+)

of +0.33e
Dipole – Dipole Interactions
• Interactions between non-charged atoms
• Hydrogen bonds are dipole-dipole interactions
Dipole– Dipole interactions are

strongly distant
and geometry dependent

Solvation of Ions
Like dissolves like
hydrophilic (Greek: hydro, water + philos, loving)
hydrophobic (Greek: phobos, fear)

Hydrogen Bonding of Common Functional Groups
The Hydrophobic Effect
Positive or zero Large and Negative Large and Negative
Endo- or isothermic Entropically driven Spontaneous

The Hydrophobic Effect
The Hydrophobic Effect – Aggregation in Water
The Hydrophobic Effect – Aggregation in Water
Amphiphiles – Mixed Polar and Nonpolar Segments
Amphiphiles - molecules have both polar (or charged) and nonpolar segments
simultaneously hydrophilic and hydrophobic
Amphipiles – Mixed Polar and Nonpolar Segments
Hydrophobic “bonds”
The hydrophobic effect acts

indirectly on nonpolar groups and
lacks directionality.
London dispersion forces between

the nonpolar groups are relatively
weak
ENTROPY
Osmosis and Osmotic Pressure
• The fluid inside cells and surrounding cells in multicellular organisms is full of dissolved
substances
• water's physical properties, the colligative properties, that depend on the concentration of
dissolved substances (e.g., lowering freezing point or raising boiling point)
• The osmotic pressure of a solution is the pressure that must be applied to the solution to
equalize the flow of water across the membrane in both directions
Dialysis: Diffusion of Solutes
• Diffusion – the movement of solutes and water across a permeable membrane
• The molecules move randomly, or diffuse, until the concentration of the solute is the
same on both sides of the membrane
• The size and type of membrane dictates which solutes move - dialysis
CHECKPOINT
• What is the relationship between polarity and hydrophobicity?
• Explain why polar substances dissolve in water while nonpolar

substances do not.
• What is the role of entropy in the hydrophobic effect?
• Explain why amphiphiles form micelles or bilayers in water.
• How does osmosis differ from diffusion? Which process occurs

during dialysis?
• Describe the osmotic challenges facing a cell placed in pure water

or in a high-salt solution.
KEY CONCEPTS
• Water molecules, which are polar, can form hydrogen bonds with other
molecules.
• In ice, water molecules are hydrogen bonded in a crystalline array, but in
liquid water, hydrogen bonds rapidly break and re-form in irregular
networks.
• The attractive forces acting on biological molecules include ionic
interactions, hydrogen bonds, and van der Waals interactions.
• Polar and ionic substances can dissolve in water.
• The hydrophobic effect explains the exclusion of nonpolar groups as a
way to maximize the entropy of water molecules.
• Amphiphilic substances form micelles or bilayers that hide their
hydrophobic groups while exposing their hydrophilic groups to water.
• Molecules diffuse across membranes which are permeable to them from
regions of higher concentration to regions of lower concentration.
• In dialysis, solutes diffuse across a semipermeable membrane from
regions of higher concentration to regions of lower concentration.

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Chemistry 114A –

Organisms on planet earth are mostly water (humans ~70%)

Water is central to biochemistry for the following reasons:

Why is water is not arranged linearly?

Water has four sp3

How many H-bonding

How many H-bonding

• Each molecule of liquid water reorients about once

• Each molecule is h-bonded to ~3.4 nearest neighbors

• H-bonds are distorted, irregular and varied

• Forms clusters of 3 to 7-membered rings

• Liquid water = rapidly fluctuating clusters

• Freezing of water – 6 regular H-bonding

• Water expands upon freezing

• Density decreases (1g/mL -> 0.92 g/mL)

Is the freezing of water

Dielectric Constant Distance

What happens when you move two charges

• Sketch a diagram of a water molecule and indicate the ends that

• Compare the structures of ice and water with respect to the

• Which of the functional groups listed in Table 1-2 can function as

• Describe the nature and relative strength of covalent bonds, ionic

partial negative charge (δ−)

partial positive charge (δ+)

• Interactions between non-charged atoms

• Hydrogen bonds are dipole-dipole interactions

Dipole– Dipole interactions are

and geometry dependent

Like dissolves like

hydrophilic (Greek: hydro, water + philos, loving)

hydrophobic (Greek: phobos, fear)

Positive or zero Large and Negative Large and Negative

Endo- or isothermic Entropically driven Spontaneous

The hydrophobic effect acts

London dispersion forces between

• Diffusion – the movement of solutes and water across a permeable membrane

• Explain why polar substances dissolve in water while nonpolar

• What is the role of entropy in the hydrophobic effect?

• Explain why amphiphiles form micelles or bilayers in water.

• How does osmosis differ from diffusion? Which process occurs

• Describe the osmotic challenges facing a cell placed in pure water

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